MPEG4, either h.264 or not (but I would go with h.264 for higher quality).
Straight from the Apple website:
Video formats supported:
H.264 and protected H.264 (from iTunes Store): Up to 5 Mbps, Progressive Main Profile (CAVLC) with AAC-LC audio up to 160 Kbps (maximum resolution: 1280 by 720 pixels at 24 fps, 960 by 540 pixels at 30 fps) in .m4v, .mp4, and .mov file formats
iTunes Store purchased video: 320 by 240 pixels or 640 by 480 pixels
MPEG-4: Up to 3 Mbps, Simple Profile with AAC-LC audio up to 160 Kbps (maximum resolution: 720 by 432 pixels at 30 fps) in .m4v, .mp4, and .mov file formats