I actually don't have an appletv, I use my MacMini hooked up to my 50" plasma running Leopard's Front Row. I hate how I have to convert my movies to mp4 in order to be used in iTunes, and I refuse to do it except for my iPhone movie files. I'm a stickler for video quality and don't want to compress something that was already compressed. I basically have all my movies on an external drive and have folders called "Movies", "TV Shows", "Music Videos", and "Other". I put aliases for these in my home "movies" folder and access it through Front Row or just through the Finder, which i end up doing 90% of the time.
For the finder I set it up in icon view with a black background. Then I find the artwork online and convert it to an icon, then apply it to the movie file. It's not quite as slick as a remote interface but I use my macmini for web/photo browsing all the time anyway, not a big deal with a wireless keyboard and mouse. It's also nice to just see all your movies all at once, and looks pretty impressive. The other thing is that Quicktime with Perian installed doesn't work smoothly with MKV files, I need to open them with VLC.
EDIT: just wanted to add that another advantage to having the macmini is that I use it as a main media basestation and for torrent downloads. My other computer is a MacBook so it's nice to have a dedicated machine for downloads and one iTunes library that is always on and that I can access at any time.