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Do the Latin stress rules (antepenultimate if penultimate is light, penultimate if heavy) have any known exceptions?
If so, what are the exceptions, and what evidence is there in the grammatical canon or in literature or poetry for them?
(Following a consensus on Latin Meta.SE, I'm reposting this question from Linguistics.SE here, as I believe the classics community may be better able to support their answer with quotations and historical context.)
Yes, there are exceptions, but fortunately not very many. Allen & Greenough has a short summary at §12.a, which I'll discuss here.
The first common exception you'll come across is a word with an enclitic (-que, -ve, -ne). With these, the accent always falls on the penult of the new word, so, using an example from Allen and Greenough, the accent for itaque "and so" falls on the 'a' itắque, though the a is still short. We can contrast that with the homograph itaque, where the accent falls on the antepenult: ítăque, though the 'i' is short, too.
While the ancient grammarians state this, some modern scholars, notably R. Whitney Tucker in the 1965 article "Accentuation before Enclitics in Latin" (TAPA 96: 449–461), dispute this by metrical analysis of Seneca's (and others') lines, since there is a coincidence of stress and length in the third foot. I quote:
[In] iambic trimeter lines (senarii), in the third foot, the long syllable of the iambus is the accented syllable of a word; or, if it is resolved into two short syllables, the first of these is the accented syllable of a word...This rule is observed also by Horace and Phaedrus, but not by Plautus and Terence.
The next exception comprises 2nd declension genitive and vocative singular nouns ending in -ius, which "retain the accent of the nominative." So, again from their examples, the name Vergilius in the genitive and vocative is Vergílī, despite the fact that the accented 'i' is short. This also applies to the genitive of neuter nouns ending in -ium.
Final-syllable-syncopated words like satin (a colloquial form of satisne or produc (the imperative of producere) that lost a terminal short 'e' are still accented as if the 'e' were never lost. So for the above examples, we get prōdū́c (older *prōdū́ce) and satín (from satísne).
Thanks to TKR below for the fuller account.
Finally, the facere compounds (e.g. benefacere, calefacere) ignore the first root and are accented as if it were only the verb. Allen & Greenough explain this by pointing out that that they are not properly compounds at all, but phrases (bene facere) which were so frequently used that the adverb lost its accent.
Imho the most comprehensive treatment of Latin accent (beautifully defined as "anima vocis" by some Roman grammarians) is Leumann, Hofmann, and Szantyr 1977, Lateinische Grammatik. Band I. Lateinische Laut- und Formenlehre. (para 235-246, Betonung und Akzent). Caveat: It is in German.
There is some evidence that even Roman grammarians admitted struggling with Latin accentology, e.g. Probus wrote this (taken from Belov 2005):
Since there is a significant number of exceptions (all of them are rara), I will focus on oxytones for now. The following is my summary of relevant parts in Leumann, Hofmann, and Szantyr 1977, Tronskii 1960, and Weiss 2009/2011.
Oxytone (final syllable accented) as a result of an apocope (of the final vowel) or a syncope of the Inlaut syllable:
a) in some proper nouns or adjectives (containing suffix *ati or *iti): Arpinas (from Arpinatis), Suffenas, Maecenas, (Valerius) Antias, Samnis (from Samnitis); nostras (from nostratis);
b) in some pronominal adverbs: illic, istic; illuc, adhuc; illinc; illac, posthac etc.;
c) in some cases with the interrogative enclitic particle ne: viden (from vides-ne), tanton (from tantone);
d) the short forms of the Perfect: audit (from audivit), intritat (from intritavit), disturbat (from disturbavit), sepeli (from sepelivi), petit, cupit, fumat;
NB: Tronskii 1960 argues such forms were rare.
e) 2SG imperative of duc and dic compounds: educ (from educe), addic (from addice)
NB: Weiss 2009 writes that such forms derived from dico are not attested in Classical Latin (p. 422, footnote 22).
Other exceptions:
f) Also, ancient grammarians insisted on oxytone stress in some conjunctions: pone (after), sine, ergo, verum (but), in some cases arguably to distinguish those from other homophones. Mancini 1997, however, seems to dispute this.
g) in some adverbs: falso, una, alias;
h) in some interjections: attat, papae (Tronskii 1960, p. 62).
If you read in Russian, I strongly recommend Belov 2005, especially Part III, where he analyzes data from ancient grammarians.
I'll just add one class to what cmw says in his excellent answer, which is shortened fourth-conjugation first-person singular perfects. Dormiī, audiī, veniī, and the like are all stressed on a short penultimate syllable, even though it's short. Like some of the other exceptions, this stress was regular before a letter disappeared; they come from dormīvī, audīvī, venīvī, and so on, which are regularly stressed.
