Apple lists this info under the specs tab for the ipad under TV and Video
"Video formats supported: H.264 video up to 720p, 30 frames per second, Main Profile level 3.1 with AAC-LC audio up to 160 Kbps, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; MPEG-4 video, up to 2.5 Mbps, 640 by 480 pixels, 30 frames per second, Simple Profile with AAC-LC audio up to 160 Kbps per channel, 48kHz, stereo audio in .m4v, .mp4, and .mov file formats; Motion JPEG (M-JPEG) up to 35 Mbps, 1280 by 720 pixels, 30 frames per second, audio in ulaw, PCM stereo audio in .avi file format"
I'm going to test this tonight when I get home from work but I assume if you bring your content into Quicktime 7 and follow those specs as a guideline you should be able to flip your video into the correct format. What I'm not sure is if you have to then bring in all that video through itunes to sync it. If that is the case I'll be sorely disappointed in the imovie app as I don't want to bring in that extra raw video into my itunes just for syncing.