Cbreak, a cool tool that automatically removes commercials from AVI files. It works by scanning the AVI for black screens, which typically come before and after a commercial, and divides the AVI into black-seperated segments. Segments that are shorter than some specified length are discarded and the rest of the frames are stitched back together, losslessly. There's also a manual mode for the chance video where this algorithm doesn't work perfectly.
If you want to do the same for MPEG files, you can still use this tool by converting the MPEGs to AVIs losslessly using ffmpeg. After using Cbreak, just convert them back to MPEG.
It's Windows only, but the source is included (GPL) so maybe this could be ported to Mac/Linux as well. Personally, I'd also like to see this modified to automatically remove the sporting event from the super bowl commercials.
Cbreak: Free commercial remover for AVI files -Link.