A couple of ideas that I've always thought would be amazing (with no idea if they are doable):
2 Player simultaneous mode for Double Dragon 1 on the NES.
Not sure if hacking Double Dragon 2 to look like Double Dragon 1 might be the easier way to do this.
Donkey Kong 94 fully colorized, like Metroid 2 or Super Mario Land's color hacks.
This one has already been mentioned multiple times, I'm sure, but either Super Mario Bros 2, the All Stars version of 2, or Super Mario Advance converted back into Doki Doki Panic.
We already have a hack of Super Mario Advance 4 that restores all the E-Reader levels. The one thing missing is patches to enable all the switch cards, such as adding Mario 2 vegetables, bosses being harder to kill, etc.
Not sure if this is possible, but I always thought it would be cool to replace the second mushroom in each Super Mario 2/All Stars 2/Advance level with a fire flower, so fireballs were available in SMB 2.
Another is the idea of adding the NES exclusive levels from the TMNT arcade game back into the arcade version and/or the SNES exclusive levels back into the Turtles in Time arcade game.
Adding the oft rumored Sheng Long to a version of Street Fighter 2 (preferably a version of SSF2 Turbo).
Make Goro, Shang Tsung, and Reptile playable in Mortal Kombat 1 (arcade or Genesis).
Make the hidden characters & bosses playable in Mortal Kombat 2 and maybe even Sonya and Kano (arcade or SNES).