In Old French and Middle English often en-, but most of these forms have not survived in Modern English, and the few that do (enemy, for instance) no longer are felt as negative. The rule of thumb in English has been to use in- with obviously Latin elements, un- with native or nativized ones.
element meaning "into, in, on, upon" (also im-, il-, ir- by assimilation of -n- with following consonant), from Latin in- "in," from PIE root *en "in."
In Old French (and hence in Middle English) this often became en-, which in English had a strong tendency to revert to Latin in-, but not always, which accounts for pairs such as enquire/inquire. There was a native form, which in West Saxon usually appeared as on- (as in Old English onliehtan "to enlighten"), and some of those verbs survived into Middle English (such as inwrite "to inscribe"), but all now seem to be extinct.
Not related to in- (1) "not," which also was a common prefix in Latin, causing confusion: to the Romans impressus could mean "pressed" or "unpressed;" inaudire meant "to hear," but inauditus meant "unheard of;" in Late Latin investigabilis could mean "that may be searched into" or "that cannot be searched into." Latin invocatus was "uncalled, uninvited," but invocare was "to call, appeal to."
The trouble has continued in English; the hesitation over what is meant by inflammable being a commonly cited example. Implume (1610s) meant "to feather," but implumed (c. 1600) meant "unfeathered." Impliable can mean "capable of being implied" (1865) or "inflexible" (1734). Impartible in 17c. could mean "incapable of being divided" or "capable of being imparted." Impassionate can be "free from passion" or it can mean "strongly stirred by passion." Inanimate (adj.) is "lifeless," but Donne uses inanimate (v.) to mean "infuse with life or vigor." Irruption is "a breaking in," but irruptible is "unbreakable."
In addition to improve "use to one's profit," Middle English also had a verb improve meaning "to disprove" (15c.). To inculpate is "to accuse," but inculpable means "not culpable, free from blame." Infestive has meant "troublesome, annoying" (1560s, from infest) and "not festive" (1620s). In Middle English inflexible could mean "incapable of being bent" or "capable of being swayed or moved." In 17c., informed could mean "current in information," formed, animated," or "unformed, formless" ("This was an awkward use" [OED]). Inhabited has meant "dwelt in" (1560s) and "uninhabited" (1610s); inhabitable likewise has been used on opposite senses, a confusion that goes back to Late Latin.
Also used with native and imported elements to form verbs from nouns and adjectives, with a sense "put in or on" (encircle), also "cause to be, make into" (endear), and used as an intensive (enclose). Spelling variants in French that were brought over into Middle English account for parallels such as ensure/insure, and most en- words in English had at one time or another a variant in in-, and vice versa.
In words from Greek, ap- is the form of apo before a vowel (see apo-).
In Latin assimilated to following -c-, -f-, -g-, -p-, and often -r- and -m-. In Old French the prefix appears in the full Latin form only "in learned adoptions of old Latin compounds" [OED], and in popular use it was represented by sous-, sou-; as in French souvenir from Latin subvenire, souscrire (Old French souzescrire) from subscribere, etc.
The original meaning is now obscured in many words from Latin (suggest, suspect, subject, etc.). The prefix is active in Modern English, sometimes meaning "subordinate" (as in subcontractor); "inferior" (17c., as in subhuman); "smaller" (18c.); "a part or division of" (c. 1800, as in subcontinent).
word-forming element meaning "forward, forth, toward the front" (as in proclaim, proceed); "beforehand, in advance" (prohibit, provide); "taking care of" (procure); "in place of, on behalf of" (proconsul, pronoun); from Latin pro (adv., prep.) "on behalf of, in place of, before, for, in exchange for, just as," which also was used as a first element in compounds and had a collateral form por-.
Also in some cases from cognate Greek pro "before, in front of, sooner," which also was used in Greek as a prefix (as in problem). Both the Latin and Greek words are from PIE *pro- (source also of Sanskrit pra- "before, forward, forth;" Gothic faura "before," Old English fore "before, for, on account of," fram "forward, from;" Old Irish roar "enough"), extended form of root *per- (1) "forward," hence "in front of, before, toward, near," etc.
The common modern sense of "in favor of, favoring" (pro-independence, pro-fluoridation, pro-Soviet, etc.) was not in classical Latin and is attested in English from early 19c.
word-forming element expressing direction toward or in addition to, from Latin ad "to, toward" in space or time; "with regard to, in relation to," as a prefix, sometimes merely emphatic, from PIE root *ad- "to, near, at."
Simplified to a- before sc-, sp- and st-; modified to ac- before many consonants and then re-spelled af-, ag-, al-, etc., in conformity with the following consonant (as in affection, aggression). Also compare ap- (1).
In Old French, reduced to a- in all cases (an evolution already underway in Merovingian Latin), but French refashioned its written forms on the Latin model in 14c., and English did likewise 15c. in words it had picked up from Old French. In many cases pronunciation followed the shift.
Over-correction at the end of the Middle Ages in French and then English "restored" the -d- or a doubled consonant to some words that never had it (accursed, afford). The process went further in England than in France (where the vernacular sometimes resisted the pedantic), resulting in English adjourn, advance, address, advertisement (Modern French ajourner, avancer, adresser, avertissement). In modern word-formation sometimes ad- and ab- are regarded as opposites, but this was not in classical Latin.