Switching from a Mac Mini HTPC to an Apple TV: what solution for watching these mkv files?
I'd recommend the Plex approach, not the Airplay solution.  If you can handle the jailbreak (ATV2 only!), it's the best approach out there for non-iTunes movies on your ATV.  And, I hate to say it here, consider the Roku, which is really cheap, officially supports Plex, and should be able to play anything you throw at it.