MediaCoder is a free universal transcoder that will quickly convert just about any audio or video file into your format of choice.
Supported video formats include H.264, XviD, DivX, MPEG-1/2/4, Flash, Theora, Dirac, H.263, RealVideo, WMV and MJPEG, and the program can handle most containers: AVI, MPEG PS, MPEG TS, Matroska, MP4, PMP, RealMedia, and ASF. MTS/AVCHD, QuickTime and OGM are supported for input only.
And on the audio side, the program can work with all the audio files you'd expect, and many you wouldn't: MP3, Ogg Vorbis, LC-AAC, HE-AAC 1/2, AC-3, MPEG Audio L2, MusePack, Speex, AMR, WMA, ADPCM, mp3Pro (input only), FLAC, WavPack, Monkey's Audio, OptimFrog, ALAC, TTA and PCM.
The program is absolutely packed with options to help you configure every step of the conversion process, and that can make it a little tricky to use, at least at first - expect to spend a while learning your way around. Once you've mastered the basics it's quite straightforward, though, and strong multi-threading support ensures your files will be converted with the maximum possible speed.
Note that the MediaCoder versioning has changed recently. For more information, see the MediaCoder blog.