Since the conversion will be in bulk, I'd recommend making direct use of
ffmpeg (powers most video converters including the aforementioned winff) or
mencoder (sister to mplayer - choose/find a build that suits) (
alt1) (
alt2).
If using ffmpeg, you're probably after a command line similar to this (audiophiles/videophiles please stop reading here):
ffmpeg -i "<input>" -vcodec libxvid -acodec libmp3lame -ac 2 -sameq -f avi "<output>"
See docs
here for any other bells and whistles you might find useful. Be warned that using -sameq is likely to make some of your videos rather large - consider modifying bit/frame rates or frame size to compensate (lossy).
Ehtyar.