This is a list of some Game-specific Hacking Tools that have been released through the ages.
(This list will probably be most helpful if we can get the obvious stuff out of the way and find some of the more obscure game-specific tools that may have nearly gotten lost.)
SOMEdit - Fully featured Secret of Mana editor created by Mop.
Lunar Magic - A Level Editor for Super Mario World by FuSoYa.
[Hyrule Magic] - An editor for The Legend of Zelda: A Link to the Past
CoilSnake - Multi-editor for EarthBound that extracts and reinserts/repoints data as opposed to directly editing the ROM