Not everyone follows the styles shown below for frequently used Latin words, abbreviations, and initialisms, but these are my usual choices. Chicago 16 instructs us to set common Latin in roman type, with sic being a notable exception. I will, however, sometimes depart from those rules for whole Latin words, depending on author, intended reader, and manuscript intentions.

ab init. ab initio (“from the beginning”).
ad hoc (“to this”). Not abbreviations. “Made for the purpose.” Sometimes italicized.
ad inf. ad infinitum (“to infinity”). As above & below, ad is not an abbreviation.
ad lib ad libitum (“at will”). Commonly without a period; rarely italicized.
c. or ca. circa (“approximately”). Chicago prefers ca.
cet. par. ceterus paribus (“all other things equal”).
cf. confere (“compare”).
e.g. exempli gratia (‘for example”). Follow with a comma.
etc. et cetera (“and so forth”). Better spelled out. Precede with comma.
et al. et alia (“and others”). Et is not an abbreviation, so is not followed by a period.
i.a. inter alia (“among other things”).
ibid. ibidem (“the same place”).
id. idem (“the same person”).
i.e. id est (“that is”). Precedes clarifications, not examples. Usually followed with a comma, but not all style guides agree.
fl. flourit (“flourished”). Used to reference the years of a person’s prime.
f.v. folio verso (“on the back of the page”).
n.b. or NB nota bene (“note well”). Follow with a colon. Often uppercase; frequently with stops. No good reason for either.
passim (“throughout”). Not an abbreviation.
percent per centum (“for each 100”). Word in American English, so not italicized.  Symbol (%) rarely used in prose text.
per se (“by itself”). Not abbreviations.
PS postscriptum (“after what has been written”). Also: PPS post postscriptum.
re in re (“in the matter of”). Not an abbreviation (no period). Usually followed by a colon.
QED quod erat demonstratum (“which was to be demonstrated”). Often treated (and punctuated) as an independent clause.
R. rex or regina (“king” or queen”). Follows monarch’s name. No following period when part of a royal cypher.
RIP requiescat in pace (“rest in peace”). I prefer to spell this out, or omit/rephrase.
sic (“thus” or “so”). Not an abbreviation. Always italicize for clarity.
s.v. sub verbo (“under the word”). As used for citing a dictionary heading.
v.i. verbum intransitivum (“intransitive verb”).
viz. videlicet (“namely”). Precedes an appositive list. No following comma.
vs. or v. versus (“against”). Use v. in specifically legal contexts.
v.t. verbum transitivum (“transitive verb”).

Obviously there are many more, but I haven’t included any Latin that I’ve never actually used or edited. Ipsa scientia potestas est!