Here is my list (from NES and SNES)
NES:
Mega Man 2 - Bubble Man Stage
Mega Man 2 - Flash Man Stage
Mega Man 2 - Heat Man Stage
Blaster Master - Stage 1, 2, 3
Ninja Gaiden - Stage 1-1
Ninja Gaiden - Stage 5-1
Contra - Stage 1
Crystalis - Outside Leaf
Ninja Gaiden 2 - Stage 1-1
Duck Tails - The Moon
Ninja Gaiden 3 - Stage 1-1
Super Mario Bros. 3 - World 1. 2. 3. 4
Gradius - Stage 1, 2
Metroid - Brinstar
SNES:
Gradius III - Stage 3, Stage 5
Mega Man X - Boomer Kuwanger's Stage
Mega Man X - Storm Eagle's Stage
Mega Man X - Sigma Fortress Stage 1
Seiken Densetsu 3 - Where Angels Fear To Tread
Super Contra - Stage 1
Super Mario RPG - Booster Tower
Chrono Trigger - Lavos
Chrono Trigger - Time of the World Revolution
Super Mario RPG - Barrel Volcano
Final Fantasy Mystic Quest - Doom Castle
Final Fantasy Mystic Quest - Battle 2
Final Fantasy Mystic Quest - Battle 3
Super Metroid - Ridley Battle
Terranigma - Dragon Castle
Ys III: Wanderers from Ys - Be Careful
Ys III: Wanderers from Ys - Valestein Castle
Actraiser - Bloodpool
Chrono Trigger - Magus
Chrono Trigger - Middle Ages
Final Fantasy VI - Devil's Lab
Chrono Trigger - Frog
F-Zero - Big Blue
Final Fantasy VI - Dancing Mad (the full thing)
And that's all I can think of!

Yea, it's alot, but I thought that they would fit with the heavy metal style of Game Over. Some of the tracks I listed can be use for a soft opening, then begin with a heavy rythem. Some of the themes can be blended together, like the Gradius stages, the Blaster Master stages, both CT's Middle Ages and Frog's theme together, etc.
And to add as a bonus, there is another one that would be awsome to hear from you guys, and it's from the Playstation (also part of Mega Man X Collections for the PS2 and Gamecube:
Mega Man X6 - Sigma Final Battle
That theme is actually a remix of the final boss themes of MMX1 and X2, so you guys can just rearranged them and make them better.
Hope to see these in the future. Hope that the ones on the poll will be in the next set of arrangement.