I would really suggest that you try Plex. The Media Center is free and the iOS app is $4.99.
You then can use your iPhone/iPad/iPod Touch to browse your library, select the video you want to play, and send it via AirPlay to your AppleTV.
It works very very well. In fact, I had a JB AppleTV 2 and moved to an AppleTV 3. I find the ATV3 and Airplay method to be more stable that using the JB ATV2.
2 negatives...
1) You need to have your iOS device handy (which for my family is not an issue as we all have our own devices with Plex installed).
2) You do not get 5.1 surround sound (my receiver does a decent job of using a logic virtual surround).
The other advantage of the Plex app is that you can actually set it up to play remotely. I've watched TV episodes stored on my home computer while sitting in a barber shop waiting for my son to get a haircut.