There are no hard-and-fast rules about the use of "cf." and other abbreviations. However, the following usages are very widespread in biologic circles, and are required by some journals:
Etheostoma blennioides: The identification is certain.
Etheostoma cf. blennioides (or cf. E. blennioides): The identification is uncertain because the material is fragmentary or otherwise flawed.
Etheostoma aff. blennioides (or aff. E. blennioides): The material is good enough to identify, but may belong to an unnamed species related to M. blennioides.
Etheostoma blennioides?: Definitely Etheostoma, but may not be blennioides.
Etheostoma? blennioides: Definitely blennioides, but this species may not belong to Etheostoma (for instance, the taxonomy of this genus may need revision.)
?Etheostoma blennioides: Both genus and species are in doubt.
You will occasionally see other abbreviations, especially in the older and more technical literature. Schenk and others (1948, Procedure in Taxonomy, p. 27-29) list three pages of Latin words and abbreviations, including the following, which have modified slightly:
aff. = affinis = having affinity with but not identical with
auct. = auctorum = of authors [that is, of various authors]
cf. = confer = to be compared to
emend. = emendatio = emended
f. = forma = form
fide = trusting [the written word of]
gen. et sp. nov. = genus [novum] et species nova = new genus and species
ibid. = ibidem = the same [reference]
incertae sedis = of uncertain position
in litt. = in litteris = in correspondence
lapsus calami = a slip of the pen
loc. cit. = loco citato = [in the] place cited [to the page]
mihi = [belonging] to me (i.e., my new species)
nob. = nobis = [belonging] to us
nom. nov. = nomen novum = new name
nom. nud. = nomen nudum = nude name (new name given without an illustration or description)
non = not
nec = nor
non vidi = I have not seen [it]
non viso = not seen
nov. = novum = new
olim = formerly
op. cit. = opere citato = [in the] work cited
partim = part
passim = here and there
pro parte = in part
q. v. = quod vide = which see
s.l. = sensu lato = in a broad sense
s.s. = sensu stricto = in the strict sense
sic = thus; [this is] so (that is, exactly as shown)
sp. = species = species (singular)
spp. = species = species (plural)
sp. nov. = species nova = new species
subgen. = subgenus = subgenus
supra cit. = supra citato = cited above
teste = according to [the spoken word of]
vide = see
Schenk, Edward T., McMasters, John H., Keen, Myra A., and Muller, Siemon William, 1948, Procedure in taxonomy (2nd edition). Stanford, California, Stanford University Press, vii + 93 p.
Also, an exclamation point (!) is occasionally used to indicate that the author has seen a particular specimen, not just read about it.