Specific group of roots can be called affixes. These roots are mostly used with some other roots in composites. However, they can form words also alone, just by adding an ending. This case is not so common as using them in composites and not all theoretically possible forms of using affixes as roots can be found in a real text.
Affixes can be classified into two groups: affixoids (more like a classical root) and true affixes.
The difference between real suffixes and classical roots together with suffixoids is following – when two roots are put together to form a composite, the first root modifies (is a determiner) the meaning of the second (main) root:
dormo|ĉambro – room for sleeping – ĉambro – room is modified by dormi – to sleep (o after the root dorm is inserted for better pronunciation – see chapter 4.3)
In the case of suffixes, the determination is done in opposite direction:
dorm|egi – to sleep deeply – dormi – to sleep is modified by the word ega – big.
The distinction between Esperanto prefixes and roots is not so obvious. The prefixes are always determining the following root. The result of such a determination can be a modification:
dis|iri – to go in different direction – the verb iri – go is modified by prefix dis.
Or a totally different meaning:
mal|bona – bad, the meaning of the word bona – good is negated by the prefix mal.
Another difference is that at least about some true suffixes (aĉ, eg, et and um), it is possible to say that they do not have inherent category and are transparent according to the category of the stem they are assigned to.
The distinction between classical roots and true affixes is not clear and depends mostly on a tradition. Different theories put the frontier between roots (and affixoids) and true affixes in a different point. PAG uses following distinction: bo, eks, ge, mal and pra are called true prefixes and aĉ, eg, et, um, nj and ĉj are called true suffixes.
For my application, the division between classical roots, affixoids and affixes is not important. It will be driven mostly by practical needs – ffixes are more often used in word building then the rest of roots, so it is good to spend more time with them. A mistake made in rules for an affixoid would produce more errors when analyzing a real text, than a mistake made in rules for an ordinary root.
I will put apart suffixes (aĉ, eg, et and um), because their transparency to the inherent category of the stem and because of different direction of modification of the meaning in composites. I will make no distinction between prefixoids and prefixes.
There are two purposes of this chapter. The first purpose is to prepare direct background for the implementation (prefixes pra and bo, suffixes io, ujo, etc). The second purpose is to show how flexible is the Esperanto word building, to show that it is hard to say that something is impossible. For this reason, the paragraph “Used as a root:” is added. Therefore some important affixes are described in separate chapter, to some is devoted only few lines.

The suffix aĉ gives to the stem shading of contempt or disgrace, detestation.
ĉevalo – horse ◊ ĉevalaĉo – nag
domo – house ◊ domaĉo – hove
hundo – dog ◊ hundaĉo – cur
paroli – speak◊ parolaĉi – tittle-tattle, twaddle
See also and mis- in chapter 4.2.3.5.

Used as a root:
aĉa – useless, ugly, aĉaĵ(ar)o – junk, lumber, aĉigi – disgust, make something terrible, aĉulo – ugly fellow, aĉularo – mob, rabble

The suffix eg augments or strengthens the idea shown by the root.
urbo – town ◊ urbego – big town, city
domo – house ◊ domego – big house, mansion
varma – hot ◊ varmega – very hot, boiling hot
necesa – necessary ◊ necesega – absolutely necessary
tre – very ◊ treege – extremely
ridi – laugh ◊ ridegi – cachinnate, guffaw

Used as a root:
ega – enormous

The suffix et is used to form diminutives.
urbo – town ◊ urbeto – small town
domo – house ◊ dometo – big house, cottage
varma – hot ◊ varmeto – warm
This suffix can be also used with the names of persons (or family members) to make intimate forms (see also suffixes ĉj, nj: 4.2.2.5)
Paŭlo – Paul ◊ Paŭleto – Paul, my bonnie
patro – father ◊ patreto – dad

Used as a root:
eta – tiny, etulo – small child, etulino – small girl, etaĵo – small thing, etigi – to diminish

The suffix um has not defined meaning. It just somehow modifies the meaning of the root. The meaning of the resulting word is hard to decode from the knowledge of the root – the only definite thing is that, they have something in common.
vento – wind ◊ ventumi – to ventilate
kolo – neck ◊ kolumo – collar
akvo – water ◊ akvumi – to water, to irrigate, to sprinkle water on
plena – full ◊ plenumi – to fulfill
Used as a root:
umo – doohickey, umi – to do something (If you can not find the right word)

Verbs created by the suffix ig mean: “to cause, to do something, to be in the state of the stem”. Intransitive verbs are changed into transitive. Verbs with this suffix are often told to be in factitive voice. The suffix ig is very often.
blanka – white ◊ blankigi – to make something white, whitewash
dormi – sleep ◊ dormigi – put to sleep
If the suffix is followed by the noun ending the result is the name of the action (pura – clean, purigi – to clean, purigo – cleaning). If the suffix is followed by an adjective ending the result is adjective with meaning doing, able to do or relating to something. (puriga – purifying, able to clean, cleaning).
The verb igi means to cause.

Verbs created by the suffix iĝ mean: “to become, to turn into”. Transitive verbs are changed into intransitive. Verbs with this suffix are often told to be in mediopassive voice. The suffix iĝ is also very often.
ruĝa – red ◊ ruĝiĝi – to become red
naski – to born ◊ naskiĝi – to be born
It is possible to form add noun ending (name of the action). Adjectival and adverbial endings are possible, but latter not very often.
The verb iĝi means to become.

The suffix ad emphasizes the process. With the noun ending, it means the name of the action, with the verbal ending, it means repetition or long lasting of the process. For verbal roots, it has the same meaning as adding simple noun ending.
martelo – hammer ◊ martelado – hammering, marteladi – use hammer often
iri – go ◊ ir(ad)o = the act of going, iradi – to be going for some time
Used as a root:
ada – continual

Suffix ec means quality. The best English counterpart is a suffix -ness. For adjectival roots, it has the same meaning as adding simple noun ending.
riĉa – rich ◊ riĉ(ec)o – richness
konfuzita – confused ◊ konfuziteco – confusedness

Used as a root:
eco – quality, characteristic, ece – in a characteristic way, eca – having the character, ecaro = karaktero – character (sum of qualities)

The suffixes ĉj (for males) and nj (for females) make from the root an intimate form. The root can be shortened – the suffix is attached after one of the first five letters.
Johanno – Jack ◊ Joĉjo – Jack
Johana – Joan ◊ Jonjo – Joanie
patro – father ◊ paĉjo – dad, panjo – mum
filo – son ◊ fiĉjo – little son, finjo – little daughter
frato – brother ◊ fraĉjo – little brother, franjo – little sister
amiko – friend ◊ amiĉjo – dear friend (he), aminjo – dear friend (she)

These suffixes are now not very often used (except few words like paĉjo, panjo) and are very often replaced by suffix et (see 4.2.1.3) or by national intimate forms (Johnny, Dick, Saŝa).

Aĵo
The suffix aĵo forms a concrete, perceivable manifestation of the root.
nova – new ◊ novaĵo – new thing, novelty
fotografi – to take photographs ◊ fotografaĵo – photography
Used as a root:
aĵo – a think

Ano
The suffix ano forms a member, participant, resident.
klubo – club ◊ klubano – member of the club
Budho – Buddha ◊ budhano – Buddhist (see also isto)
Used as a root:
ano – a member of a club, society, ani – to be a member, anigi – to make somebody a member of something, aniĝi – to become a member, aneco – membership, aniĝilo – application form, etc.

Aro
The suffix aro adds to the root the meaning of a collection.
arbo – tree ◊ arbaro – forest
homo – man ◊ homaro – mankind (≠ aro da homoj – group of people)
Used as a root:
aro – group, ara (adj.), are (adv.) – in groups, grandare – in big groups, ari – to be in group, ariĝi – to group oneself, arigi – to group somebody

Ejo
The suffix ejo means place where something is performed or where something is kept, a building, etc.
lerni – to learn ◊ lernejo – place for learning, school
preĝi – to pray ◊ preĝejo – a church, musk, etc (kirko = church)
ministro – minister ◊ ministrejo – department
Used as a root:
ejo – place

Ero
The suffix ero means an element of the thing expressed by the root. Not nominal stems are automatically nominalized (as if suffix aĵo were added).
pano – bread ◊ panero – a crumb of a bread
neĝo – snow ◊ neĝero – snow flake
kudri – to sew ◊ kudrero – a stitch
Used as a root:
ero – element, grain, ereto – small element, grandera – coarse-grained, diseriĝi – to disintegrate (intransitive), diserigi – to cause to disintegrate

Estro
The boss of the thing expressed by the stem.
ŝipo – ship ◊ ŝipestro – captain
urbo – town ◊ urbestro – mayor
The boss of some group of people can be expressed also by prefixing the root ĉefo – chief.
Used as a root:
estro – boss, estri – to direct, estraro – board of directors

Ido
The suffix id forms an offspring, young creature, etc.
hundo – dog ◊ hundido – puppy
planto – plant ◊ plantido – small plant
latina – Latin ◊ latinida lingvoj – languages with the Latin origin
Used as a root:
ido – offspring, ideto – small young, idaro – all descendants

Ilo
The suffix il means a tool for doing whatever is expressed by the preceding root.
tranĉi – to cut ◊ tranĉilo – tool for cutting, a knife
komputi – to compute ◊ computilo – a computer
butero – butter ◊ buteri – to butter ◊ buterilo – knife for buttering
linio – line ◊ linii – to line ◊ liniilo ◊ ruler
Used as a root:
ilo – instrument, ilaro – set of tools, ilujo – box for tools, ilejo – workshop

Ino
The suffix in means a female.
patro – father ◊ patrino – mother
bovo – cow ◊ bovino – she-cow
Esperanto is a sexist language. Most of roots with meaning of human beings are of the male sex. Today more and more of them are considered neutral. Especially professional titles are neutral. The male equivalent of this suffix is a prefix vir-, it can be added to roots which sex is neutral.
kato – cat ◊ virkatino – tomcat

Ingo
The suffix ingo has a meaning of a holder for the thing described by root.
kandelo – candle ◊ kandelingo – candle-holder
Used as a root:
ingo – holder, mostly sheath, ingi = eningig – to put into the holder, sheath, malingi = elingigi – to put out of the holder, unsheathe

Ismo
The suffix ismo has a meaning of a doctrine, movement, system, etc.
Budho ◊ budhismo, Markso ◊ marksismo
ĵurnalo – newspaper ◊ ĵurnalismo – journalism
Used as a root: ism – movement, doctrine

isto
The suffix isto has a meaning of an individual professionally occupied with something, somebody who is used to do something. The suffix can be also used as equivalent for two suffixes ist|ano. This is not used if the ismo is added to the member of the movement, etc. (krist|ano – Christian ◊ kristanismo – Christianity).
labori – to work ◊ laboristo – a worker
lingvo – language ◊ lingvisto – linguist
Budho ◊ budhisto, Markso ◊ marksisto

Ujo
The suffix ujo has three meanings:
1) A container or box for something. This is the main meaning.
papero – paper – paperujo = paperkesto – box for paper
salo – salt ◊ salujo – saltcellar, saltshaker
2) A tree having fruit or flowers specified by stem. This meaning of the suffix is rather archaic, today it is replaced by forming a composite with arbo – tree or arbeto – small tree.
pomo – apple ◊ pomujo = pomarbo – apple-tree
3) A country for the nationality expressed by the stem. See chapter 4.3.4 Names of countries.
Italo – Italian ◊ Italujo = Italio – Italy
When the suffix ujo is used as a root, it has the first meaning – a box or container.

Ebla
The meaning of suffix ebla is “suitable for being done”.
legi – to read ◊ legebla – readable
fari – to do ◊ farebla ◊ possible to be done
Used as a root:
ebla – possible, possible to be done, eble – maybe, eblo = ebleco – possibility, eblaĵo – possible thing, possibility, ebligi – enable, ebliĝi – to become possible, malebla – impossible

Ema
The meaning of the suffix ema is “to have tendency or inclination to do the thing described by the stem.”
labori – to work ◊ laborema – industrious
dormi – to sleep ◊ dormema – sleepy
Used as a root:
ema – inclining, emo – inclination, emi – incline, emiĝi – to become inclining, emigi – to cause that something is inclining

Enda
The meaning of the suffix enda is “it must be done the thing described by the stem”
skribi – to write ◊ skribenda – that must be written
vidi – to see ◊ videnda – that must be seen
Used as a root:
enda – mandatory, endo – necessity, endi – it is necessary

Inda
The suffix inda has meaning “worthy -ing”
fari – to do ◊ farinda – worth doing
vidi – to see ◊ vidinda – worth seeing
Used as a root:
inda – worthy, indi – to be worthy, indigi – to make something worthy, malinda – to be unworthy, senidulo – unworthy man

Bo marks relative by marriage. In English, the same thing is done by adding in-law.
bofrato – brother-in-law, bofilo – son-in-law, bopatrino – mother-in-law, bokuzo – cousin-in-law, bonevo – grandson-in-law, etc.

The exception is a word for child coming from the previous marriage(s) of one of the spouse – it is marked by prefixing duon^[31].

Bo can be also used in following words:
boparenco – relatives by marriage
bofamiliano – member of the family by marriage
boedziĝi – to marry with the wife of one’s dead brother (used by Zamenhof in the translation of Bible)
boamiko – jocular way to call friend of one’s spouse

There is no distinction between relatives got by one marriage and relatives got by two marriages: mia bofrato is brother of my spouse or husband of the sister of my spouse.

If bo is together with prefix ge (see 4.2.3.2), bo stands before ge^[32]: bogefratoj – brothers-in-law and sisters-in-law.

The prefix as a root:
boulo = boparenco – relative-in-law, boeco = boparenteco – the type relation between two relatives-in-law, boa – being of the in-law type of relation

Ge marks both sexes. This prefix is used before roots of male beings or roots that are neutral from the point of the sex.
geknaboj – boys and girls, gejunuloj – young people, youth, geinstruistoj – teachers of the both sexes
For neutral words, the prefix is very often not necessary. Words like lernantoj (pupils) or doktoroj (doctors.) are good enough for describing beings of both sexes and the prefix ge is used only for stressing the fact that people in the group are of both sexes.
The plural after the word with this preposition is common, but not necessary: geedzo – spouse, gepatro – parent.
The meaning of the prefix can be slightly different, depending on context:
1) A pair (e.g. of husband and wife): gepatroj – mother and father, parents, geonkloj – uncle and aunt, geedzoj – husband and wife, geamantoj – lovers.
2) Members of the same type, but both sexes of a family: gefiloj – sons and daughters of the same family.
3) The whole family: geurbestroj – the family of the mayor

Prefix ge is also used with things that do not have sex. In that case, it means that the things are related with both sexes: gelernando – coeducation, gelernejo – coeducational school. However, this usage is quite rare.

As root:
geo – he and she, pair, gea – mixed, etc. (gea lernejo = gelernejo – coeducational school), geiĝi = pariĝi – make pairs from oneself, geigi = parigi – to pair

Prefix mal denotes total opposite to the stem.
malbela – ugly, malvarma – cold, malgranda – small, malrapida – slow, malami – hate, malaperi – disappear, malamiko – enemy, malantaŭ – behind.
Prefix mal is very often used. In the beginnings of the language, it was nearly the only way of finding an opposite for most of the words. Even very common words (malgranda – small, malfermi – open, malnova – old, etc) had to be expressed using this prefix. Today, some synonyms to the mal- words exist, some of them are used more and some of them less often: fini = malkomenci – finish, frida = malvarma – cold, breva = mallonga – short, eta = malgranda – small, dura = malmola – hard, cis = maltrans = on this side (trans – across), olda = malnova – old, etc.

As a root:
malo – opposite (noun), mala – opposite (adj.) male – opposite (adv.), oppositely, malinda – undesirable, unwelcome, etc.

Prefix pra has following meanings:
1) With names of relatives, one generation older or younger: praavo – great-grandfather, pranepo – great-grandson, praonklo – great-uncle. The prefix pra can be even repeated: prapraavo – great-great-grandfather. For the father of the father and for the son of the son are words avo and nepo – prapatro and prafilo belong to the second category.
2) Very distant in time (mostly in the past – ancient or primeval): praarbaro – primeval forest, pratempo – primeval ages, prahistorio – prehistory, prabesto – primeval animal, prahomo – primeval human, prapatro – founder of the family, of the kin or nation, prafilo – descendants after many generations.

As a root:
prae – primevally, praa – primeval, praeco – “primevalness”, praulo = primeval ancestor, forefather

Eks
Eks marks something former. It is mostly used in front of the word with the meaning of some profession or function.
eksprezidanto – ex-president, eksposedanto – former owner, eksdirektoro – former director, eksurbestro – former mayor, eksedzo – former husband, eksedziĝi – to divorce oneself, eksmoda – out of the fashion
Eks used as a root: eksigi – to force somebody to abdicate, eksiĝi – abdicate, leave a club, eksa – quondam, abdicated, eks! – Eks pri la reĝo! – Away with the king!

Dis
Prefix dis means separation in different directions, scattering.
iri – to go ◊ disiri – to go in different directions
vojo – way ◊ disvojiĝo – road-fork

Ek
Prefix ek means the beginning or ephemerality.
iri – to go ◊ ekiri – to start to go, to set out
krii – to shout ◊ ekkrii – to shout out
Ek can be also used alone as an interjection: Ek! – Let’s start!, Ek al li!^M – Let’s catch him. Or as a verb: eki = komenciĝi – start (intransitive), begin, ekigi – start (transitive)

For
Prefix for means removing, disappearing, distance, spoiling.
iri – to go ◊ foriri – to leave
dormi – to sleep ◊ fordormi – to spoil time by sleeping

Mis
Prefix mis expresses an error or incorrectness. In contrary to the suffix aĉ, this prefix is used in objective stating.
kalkuli – calculate ◊ miskalkuli – miscalculate
traduki – translate ◊ mistraduki – mistranslate
kompreni – understand ◊ miskompreni – misunderstand
Mis used as a root:
misa – incorrect, erroneous, misi – to err

Re
Prefix re means returning or repetition.
veni – to come ◊ reveni – to come back, to return (intransitive)
meti – to place ◊ remeti – to put back, to return (transitive)
legi – read ◊ relegi – read again
Re can be used alone in ree – again, reen – back, rea – adjective from ree or reen.

There are also many unofficial affixes. I list only the most often ones:
-iva – capable of doing something
produkti – product ◊ produktiva – productive
-eska – similar to, or in the manner of
japano – a Japanese ◊ japaneska – Japanesque
-ala – is used to derive adjectives from nouns derived from adjectives
varma – hot ◊ varmo – heat ◊ varmala – thermal
-oida – resembling; having the appearance of; related to, mostly technical
antropo – human ◊ antropoido – anthropoid
-oza – full of
poro – pore ◊ poroza – porous
-iza – to apply something (thing or method) to an object
salo – salt ◊ salizi ion – add salt to something
retro- – in the opposite direction
iri – go ◊ retroiri – to go in opposite direction

There is also large amount of affixes used in some special field – in chemistry (-oza – feroza – ferous, -ika – sulfika – sulfuric, etc), in botany, medicine (-ozo – sklerozo – sclerosis, -ito – dermatito – dermatitis) and so on.

Some of the unofficial affixes are partly so called pseudoaffixes. They are mostly affixes in the languages the Esperanto vocabulary comes from.
Many of Esperanto roots are composites in the language they come from. Therefore, some roots start or finish with the same sequence of characters. These sequences look as an affix. However, the rest of such a word is very often not an Esperanto word. On the other hand, sometime new words are created connecting these sequences with Esperanto roots. These elements are called pseudoaffixes (pseŭdoafiksoj).
Typical example is a pseudosuffix logio: ornitologio – ornithology, zoologio – zoology, etc. However, there are also words metodologio – methodology (metodo – method), antropologio – anthropology (antropo – human). And there are also purely Esperanto words: esperantologio – science about Esperanto, birdologio – ornithology, formologio – morphology, etc. In these words is a suffix ologio.
Another pseudosuffixes are iko (poeto – poet ◊ poetiko – poetics, stilisto – stylist ◊ stilistiko – stylistics), acio, icio (delegacio – delegation, operacio – operation, pozicio – position, etc) and many others.
There are also pseudoprefixes: aŭto (autobiografio – autobiography, aŭtomobilo – car, aŭtonomio – autonomy, aŭtokrato – autocrat), anti (antikristo, antisemito), eŭ (eŭfemismo – euphemism, eŭgeniko – eugenics) and others.
Most of these words are treated as separate roots in Esperanto. Some of them can be considered as unofficial affixes (ologio, iko). In contrary to classical affixes, these cannot be used systematically (sometimes is ok ologio, sometimes iko).

^[31] See chapter 3.7.2.6 - Fractions.
^[32] This is opinion of the PAG (§417). PMEG (bo) is not so strict, it states that the order of the bo and ge does not matter, and that it is only a habit to put ge first.