Very few words come to mean their exact opposites via misuse. (I am assured that "bad" meant "good" in some brief period of the 80s in which I was too young to know the cool slang, but it wasn't because people were confused about which meant which.)
Language is living, breathing and constantly changing. Words mean what people intend them and understand them to mean, not necessarily what they mean ... uh ... literally.
Wikipedia used to have a good list of them, but it looks like they just deleted it. Thank god for revision history: http://en.wikipedia.org/w/index.php?title=List_of_auto-anton...
"Usage Note: For more than a hundred years, critics have remarked on the incoherency of using literally in a way that suggests the exact opposite of its primary sense of "in a manner that accords with the literal sense of the words." In 1926, for example, H.W. Fowler cited the example "The 300,000 Unionists will be literally thrown to the wolves." The practice does not stem from a change in the meaning of literally itself -- if it did, the word would long since have come to mean "virtually" or "figuratively", but from a natural tendency to use the word as a general intensive, as in They had literally no help from the government on the project, where no contrast with the figurative sense of the words is intended."