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Super Metroid
Super Metroid has been extensively hacked.
Utilities
SMILE is a work in progress by Jathys. It currently has support for editing rooms, item placement, enemy placement, enemy attributes, music selection, auto map, and more.
Hacks
There are currently three popular, complete hacks of Super Metroid. Super Metroid: Redesign is the largest and most extensive hack. It features new physics, a world roughly twice the size of the original, new events, a few new items and abilities, and some bug fixes. It's considered very hard, and easy to get lost and stuck in, but does not allow the player to get stuck unintentionally.
The other two popular hacks are Limit and Legacy. Limit is the top middle link, and Legacy is the top right link. Both were made entirely with SMILE.
Legacy retains most of the feel from the original Super Metroid with basically the same sequence of events, making several changes to room layout and the overall map. It is only slightly more difficult than the original Super Metroid.
Limit drastically changes the map and layout, and adds several twists and challenges. It's considered a very hard hack to beat.
Two major hacks are currently in the works: Alliance by Jathys, the author of SMILE, and Insanity by Kejardon, most well known for finding glitches and tricks in Super Metroid.
Miscellaneous
There are only two versions released: NTSC and PAL. The PAL version has a number of discrepencies due to speed changes.