If you have a recent ATI video card, I think their current driver comes with a video conversion software. I'm not sure how good it is, but I'd assume it uses the GPU to accelerate things considerably. It's worth looking into at least.
Nvidia has something similar. It's a third party program called Badaboom that makes use of CUDA. It's what I currently use to convert videos for my Hero, mostly just because it's fast (20 minutes for a 2hr movie). That one isn't free though.