I want to highlight a few mods (because this question will come up eventually :-) ):
Alex Kidd in Miracle World_
- Snappy Snorg and the Seven Silver Stones: Total conversion with different graphics and gameplay, including puzzles. High quality.
- Octo Unleashed: Impressive conversion with good graphics and atmosphere.
- Stella in Adventure World: A more traditional style of gameplay with new character, story and level designs.
- Voyage - A Sorceress Vacation: Total conversion with new gameplay, character, graphics and story.
Sonic_
- Boxguy Adventure 2: Part of a multiplatform series. Play as a new character within its own levels structures.
- NC Revision: Keeps main game intact, but updates graphics to very beautiful style. Other improvements in gameplay and miscellaneous alterations are made as well.
Sonic 2_
- Frenzy: 7 zones with secrets and alternate paths, making up to 21 levels. Further some changes to graphics and musics as well.
- Zen Island: Main game stays intact, but with changes to graphics palette, music and and a little bit on gameplay.
Phantasy Star_
- Makeover: Redesigns graphics (including Character Sprites Improvement hack) inspired by graphics from PlayStation 2 Phantasy Star Generation 1.
- Easy Patches (Double Meseta and XP): Collection of patches to reduce the grind. Simply double the money and xp earned from battles.
Super Boy 4_
(Note, Super Boy 4 is an unlicensed game in Korea that is a bad knock-off clone of Super Mario games. It has this uncanny effect of Mario games, but just in bad and wrong.)
- Individuality Improvement: Changes the graphics to something new and unique, getting rid of or the Super Mario aesthetics. Or makes changes so it looks a bit more unique than before.
Wonder Boy 5 Monster World (E)_
- Sram Pad Enhancement Hack: Adds a save function so you don't need to use passwords (or save states). Coloring are also adjusted, as the original colors can be ugly.