MARSONIST I've used or attempted to use just about any application you can imagine to try and convert videos and find that VisualHub is the perfect mix of power and usability. I've used FFmpegX, but get bogged down in the option and end up trying 3 or 4 times before finally getting the results I'm looking for. VisualHub seems to take care of of the details for me and has, so far, given me great results every time on the first try.
I was getting some errors while attempting to preview files, but I see that as of today there is a new "dot" release that will hopefully fix that. Even if it doesn't this program is heads and shoulders above everything else I've tried.
(Version 1.0.1)