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
An overworld Map Editor for BS Zelda Map 1 and Map 2, this can also view the Underworlds.
A Dungeon Editor for BS Zelda: Inishie no Sekiban that was used to restore the dungeons in the Ancient Stone Tablets ROM restoration project and it's source code
Super Metroid Integrated Level Editor by Jathys (discontinued)
SMILE JX by JAM (Continued version)
CoilSnake - Multi-editor for EarthBound that extracts and reinserts/repoints data as opposed to directly editing the ROM