Miro Video Converter

Miro Video Converter is a FREE (and Open Source) transcoding app. So far it looks good for its intended purpose.

Here's a list of it's capabilities so far:

Convert to MP4 Video
Convert AVI to MP4
Convert H264 to MP4
Convert MOV to MP4
Convert WMV to MP4
Convert XVID to MP4
Convert Theora to MP4
Convert MKV to MP4
Convert FLV to MP4

Add that it'll also transcode to Ogg Theora (video) and it's a pretty handy app.