My thoughts are (and they're all Linux games):
[3842] Linux Axiom Verge by keylie in 27:44.38 - by the end of the game you're chaining multiple movement abilities at a pace far faster than any human can hope to keep up with.
[3809] Linux Mari0 "Portal mappack" by lexikiq, Masterjun in 03:05.23 - you can build up very high speed by flinging yourself through portals, even to the point of clipping through walls simply because you travel too fast.
[3841] Linux Order of Twilight by lexikiq in 00:47.23 - teleport spamming moves Twilight far faster than any human can keep up with. (Does repeated teleporting count as fast movement, or does it have to be continuous and differentiable to count as 'speedy'?)
[3827] Linux SteamWorld Dig 2 by keylie in 18:11.87 - has several physics glitches that produce absurd speed.
re: Towerfall: My understanding is that the physics glitches still produce superhuman amounts of speed even at 60FPS, they just get slightly stronger at high FPSes. keylie produced a chart comparing how fast hyper jumps are at different FPSes here:
http://tasvideos.org/forum/viewtopic.php?t=20479 And it looks like 1000FPS is only ~25% faster than 60FPS.