It's a lengthy process, but I agree with the convert/tag/import to iTunes suggestion. I'm still in the process of finishing it now, but I can't even begin to describe how satisfying it is to open iTunes and see a beautiful array of movies and TV shows, only to be superseded by the glory that is turning on my Apple TV. *heavenly chorus*
Either hack the AppleTV and install ATVFiles, like I have done, or convert them to mp4. A good conversion program, if you are using a Mac, is Visualhub