I've been having a bit of trouble adding some movies to my iTunes library this evening - in that I'd have to convert a movie to a .mov file in order to import it at all.
A few google searches away and I'd found the answer to all my problems. If you have the Apple development tools installed (and are obviously on a Mac), you can simply change the file meta-data of the movies via the terminal in order to allow you to import them. It's very simple to do:
SetFile -t "MooV" movie.avi
Via: AVI to iTunes on MacRumors Forums
I did, however, have to change the iTunes settings so that it didn't take it's own copy of the files when importing them. I have a separate Movies folder for a reason thank-you-very-much iTunes.