Currently in beta, Permute for the Mac has been running on the 27″ iMac i5 in the background for a good 12 hours straight without a flaw converting a bunch of video files to pack into iTunes for viewing on the iPad.
Preset formats include iPhone, AppleTV, Xbox, PS3, and you can even create menu-less chapter-less DVDs which are saved as ISOs on your Mac. Using the simple drag-and-drop interface, just add in your media, select a preset you want to convert to, and hit convert. It uses the FFMpeg engine making it faster in most cases than the QuickTime engine many of the others use.
$14.95 well spent.