First, it's nowhere near as simple as I thought. Second, it's nowhere near as complex as I thought. Well, here's how it works. MPEG-4 is a way to define a codec. So, when you go into quicktime and it says, save as MPEG4, you're not saving as MPEG4, you're saving as "Apple's MPEG-4 codec". Which, by the way, sucks compared to basically any other option . There's actually a whole bunch of MPEG-4 codecs, including Divx, Xvid, 3ivx, and a whole bunch of high end professional codecs that cost a lot of money. In theory, any MPEG-4 player can play any MPEG-4 codec. In practice, not so much. But also, in practice, VLC and MPlayer can play them all.
Following all that, here's an enlightening discussion thread comparing various formats and explaining MPEG-4 .