Thank you! this works very well... although it is the first video encoding program I've tried.

Actually, could you add an option to just have it say what commands it is passing to mencoder? I want to use the -aid 1 and -sid 0 flags, but can't pass those using the nice gui. (That would change the audio language and display subtitles on the OGM files I am converting.)

I can get it to change the aid using ~/.mplayer/mencoder.conf, but not the subtitles.
*edit* Actually, I can't get mencoder to do subtitles at all -- so the problem isn't with mediaconverter2.