I was using ffmpeg, but now, I'm giving VisualHub a whirl. So far, it's doing a nice job, and doing it pretty quickly and easily. I read somewhere that VH is simply a front end for ffmpeg, making it a bit more user friendly, but I don't know if that's the case (about it being the front end).
I like how it has a preset for AppleTV, and it'll import the finished file into iTunes, too.
PS
I can confirm it's a front end for ffmpeg! Activity Monitor lists its process as "vh123ffmpeg."