Personally, I'd download OpenShiiva (check VT), and use that. It produces MP4 video files that are quicktime compatible, and with the XviD codec (which is playable in QT with the 3ivx codec) they look spectacular at very low bitrates.
If you have QT Pro, you could also just use Apple's MP4 compressor--it actually works quite well, and in my experience produces much better files than Sorenson 3, though with Cleaner you might get better results with Sorenson 3.