BS-Zelda - MottZilla Patch  This is a huge patch for BS-Zelda. Read more about it at the BS-Zelda Homepage. Features like a Title screen, front end menu with 3 save slots, and endings are some of the features in the patch.
Ninja Gaiden III - Restored  This hack restores enemy damage to match the Japanese version and grants unlimited continues and adds new password system programming so it is named the Restored version. With these 3 major changes this version is the one to play since it finally is on par with the Japanese version. The original US release and the SNES rerelease each have their drawbacks.
Mega Man X (SNES) - Debug Menu  MMX contains a hidden Map Editor that is fun to play around with however it has no normal way to access it. It was only possible with a PAR code but with this Debug Menu hack you can use the Map Editor as well as some other features to mess around or test your Level hacks.
Mortal Kombat II (SNES) - Hidden Characters Playable  MK II normally crashes when playing as the hidden characters Smoke, Jade, and Noob Saibot. And there is no normally accessible way to play as them. This hack allows you to play as all 3, complete with special moves and fatality moves. To avoid being redundent Noob has Sub-Zero's moves while Smoke retains Scorpion's moves. During Versus battle or endings the game will default to showing Kung Lao instead.
Mega Man - The Wily Wars SRAM Save Hack  MMWW was released in Europe and used Serial EEPROM saving. Unfortunately most emulators and programmable cartridge devices only support typical battery backed SRAM. This hack changes out the saving routine with one that uses SRAM instead.
Wolverine - Easy Version  Wolverine is a challenging game in part because it has no mercy for any mistake. This hack adds a small recovery time after being damaged before you can be damaged again. The game is still challenging but should be more fun and easier for players to complete.
Zombies Ate My Neighbors - Debug/Cheats  This hack adds the ability for player one to modify their inventory while the game is paused as well as the ability to make the exit appear.