In alphabetical order by system:
NES Batman by Jecy
One of my favorite games when I was a youngster. Seeing it played so well brings a tear to the eye.
NES Gauntlet by FODA
Another game I spent years playing. I didn't even realize it had an end!
NES Metroid any% by Zoizite
This is officially the first game I ever did a speedrun of, at about the age of 10. I was pretty boastful of my 20 minutes too.
NES Rygar warpful by Walker Boh
I also owned this game, but I gave up on it because it was too hard.
NES Snake Rattle'n Roll by Nitsuja
The mobility in this game is unreal. This game is a lot harder than he makes it look, especially the under water levels.
SNES Donkey Kong Country 101% by Arnethegreat
Diddy can fly? Omgwtfh4x0rz!111!!eleven!
SNES Mega Man X & X2 by DeHackEd
I've never played either of these, but this video is absolutely amazing. Perhaps it will inspire similar runs?
SNES Super Metriod 100% by JXQ
What can I say? I'm a huge Metriod fan, and this still remains the best of the series imho. JXQ's run does it the justice it deserves.
Genesis Sonic 3 & Knuckles by SprintGod
The very embodiment of fast paced, SprintGod utilizes both unintended and unexpected routes to make this game even faster. Don't blink!
N64 Super Mario 64 by Spezzafer
I'll quote myself after the first time I watched it: "That's the most amazing thing I've ever seen in my life."