There's a nice little front end GUI program for the ffmpeg video converter called Avanti which seems to be getting some attention at videohelp.com:
http://forum.videohelp.com/topic343287.html#1833980
As far as GUI front ends for ffmpeg go, I'm a fan of Winff, but Avanti looks like it gives the user much more control of the conversion.
From what I can gather, you need to install your own copies of ffmpeg and avisynth (both freeware) and set the menu accordingly in Avanti.
Link to ffmpeg (the link above links to an avisynth download):
http://www.videohelp.com/tools/ffmpeg
(I prefer downloading from the actual author's site, and those links are provided by videohelp.com, too.)
Both Super and Mediacoder use the ffmpeg and mencoder conversion tools, but from perusing their forums, I gather that divx and xvid synchronization problems are not uncommon, with various solutions offered. I'm not sure how successful either program is in correcting a/v synch, though. Has anyone tried Avanti?