Personally, I use AVS Video Converter for all video conversion, I used it to convert all my DVD rips from .avi to .mp4's for my iPod. 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.
If you want a try,here:
http://www.flash-video-soft.com/avs-video-converter/
hope it is useful