Metroid games are all pretty great. Even today, many gamers still playing them (i am talking for the 8/16 bit games and from the GBA, as the rest are trash). There are many modders who are releasing some cool hacks, giving a different view in those gems.
Note: These mods requiring the emulators and the rom of the game to run. These are not the "best" mods, but the mods i tried. There are many other great mods, too.
Metroid Super Zero Mission (Snes)
Super Zero Mission comes with many controlling improvements and requires nothing more than the Samu's basic abilities in order to finish it. However, pro gamers can test all the Samu's abilities. The package contains two versions of the hack, an easy and a hard. The game is difficult even by using the easy hack.
Super Metroid - Escape2 (Snes)
Is a level hack of Super Metroid and changes the levels and the colors of the game.
Super Metroid Legacy (Snes)
A full Super Metroid hack, worth to try. Contains new maps and different item and enemies positions. Has the same difficulty with the original game.
Super Metroid: Hydellius (Snes)
This hack contains new enemies, new levels and backgrounds and more. I didn't like the color of the background.
Super Metroid Cristener Homenag (Snes)
This hack was the best of the 2013.
Super Metroid: Sunshine (Snes)
Is a full Super Metroid hack, with a complete different layout, except the items which, according to the creator of the hack, do not have significant changes. Though it's an easy hack, it requires some special skills in order to finish it 100%.
Ice Metal 1: Uninstall (Snes)
A hack which is centered in exploring and find the items, without being difficult to finish.
You can try and the Super Metroid Redesing.
Metroid Incursion (NES)
A hack for the classic Metroid (NES), which has improved graphics, new level desing, better sprites of the characters and more.
Metroid Rogue Dawn
The same modder is preparing the "Metroid Rogue Dawn", which have even better design. Also for the NES Metroid.
Super Metroid Advance (GBA)
A mod that transfers the Super Metroid's experience to GBA.
Metroid II DX (GB)
This mod inserts color into original Metroid II (GB). Runs start to finish on the real hardware without and major issues.