I've watched all four of these again (not including NES Super Zzzzz Bros.) and I think that this was an excellent list. I don't think more nominees would have helped the process; in fact, I think the large amount of nominees in some categories harmed the voting.
I liked my Super Metroid a lot, though I greatly prefer the
no-cutscenes AVI, which has spoiled my attention span even farther than TASing already has. Super Mario 64 was very good as well; not so much for the 0-starness, but the stylistic choices made were very nice. Sonic 3 has always been a little too glitchy for my taste, but it's still a very good watch.
However, I'm voting for Metroid Zero Mission. There's so much available in what the main character can do that perfecting those abilities is very fun to watch, and the style and movement was excellent throughout. It also reminded me of how good of a TAS that Super Metroid: Redesign would make, and I'm looking forward to that.
(I'm sorry if it's weird that I didn't vote for my own movie)