I've read that some prefer MKV containers for all their DVD encodes. I've been using MP4 (working on SD DVD's, I'll use MKV for my BD's). I know that the Apple TV 2 doesn't play MKV files, I have my Apple TV 2 JBen and using XBMC so compatibility there isn't an issue. The only issue is with iDevices and non-JB'en items. I plan on ditching my DVD's once encoded so getting the encodes near lossless (don't care about size) is more important, but I'm curious why MKV may be better than MP4.