Ideofact is "deeply disturbed that there's a whole school of crackpots out there that, lo these many years," he has "been blissfully unaware of", followers of a German scholar who claims (to quote Travelling Shoes) "that the years 614 to 911 AD simply did not exist; that the Holy Roman Emperor Otto III, together with Pope Sylvester II and Byzantine Emperor Constantine VII, added nearly 300 years to the calendar, primarily for occult reasons" -- not to mention inventing Charlemagne.

Here are four favorite examples from the field of Classics:

1. Some 19th century scholars alleged that some or all of the surviving works of Tacitus were forgeries composed in the 14th century by the humanist Poggio Bracciolini. The fact that there are huge gaps in Tacitus' Histories and Annals proves nothing either way: Poggio might have left such gaps for verisimilitude, or to save the trouble of composing the missing parts. But why are so many of the best parts missing? Not that we can be sure they were the best parts if they're missing, but surely Poggio wouldn't have omitted the death of Nero, the entire reign of Caligula, and the destruction of Pompeii and Herculaneum by Vesuvius. For the last, we even have Tacitus' source in the letters the Younger Pliny (an eyewitness) wrote to him, which would make composing a Pseudo-Tacitean version that much easier -- and more interesting. (Actually, that would be a good exercise for an advanced Latin prose composition course.)
2. Then there's what a friend calls the 'Blonde Athena' hypothesis. The basic argument of Homer in the Baltic is that the geography of the the Iliad and Odyssey has nothing to do with the Mediterranean but actually refers to various sites in the Baltic Sea, and a war that occurred there before 'blond Menelaos' and his Viking friends relocated to Greece. Many amusing identifications are offered with every appearance of sincerity: Troy is a small town west of Helsinki, Naxos is Bornholm (a Danish island off the coast of Poland), Achilles' homeland of Phthia is southeastern Estonia, Odysseus' four islands are in southeastern Denmark, Pelasgians are Poles, the Nile is the Vistula, and so on. Much of the argument is based on pseudo-etymologies such as "Pelasgoi" = "Polska".
3. Members of the Calpurnius Piso (pronounced 'Peace-oh') family are prevalent in Roman history, including Caesar's wife Calpurnia, the dedicatees of Horace's Ars Poetica, and the leader of the largest conspiracy against Nero. But there seem to be dozens of sites involved in an elaborate theory that various Calpurnii Pisones invented Jesus and that the entire New Testament "was authored by members of an aristocratic Roman family to keep slaves under control and submissive". There is a summary at this site, but you apparently have to buy the book to get the whole theory. There is an amusing anti-Piso site here: I particularly like the file name.
4. My favorite of all these is the theory that the Gospels are loose translations of a lost tragedy of Seneca, the Nazarenus. This theory is summarized briefly at this site and more fully here.