Personally, I use AVS video converter for all video conversion. Its a commercial solution and cost about $39 US dollars, It will convert from just about any format to just about any format. I used it to convert all my DVD rips from .avi to .mp4's for my iPod. It has full Apple TV support so it can convert your files for you with ease. Here's some of the features from their site:
Convert Video between Almost Any Formats:
HD Video (inc. AVCHD, MPEG-2 HD and WMV HD), TOD, MOD, M2TS, AVI (DivX, Xvid, etc.), MP4 (inc. Sony PSP and Apple iPod), WMV, 3GP, QuickTime (MOV, QT), SWF, DVD, VOB, VRO, MPEG-1, 2, 4, H.263, H.264, Real Video, DVR-MS, MKV, FLV etc.
http://www.flash-video-soft.com/avs-video-converter/
hope it helps