There are a ton of fan-made games and romhacks that I've played. I'll list the good ones that I can remember:
Super Mario RPG: Revolution (It's still Super Mario RPG, but with extra content added and the level cap is raised from 30 to 50; it's also more difficult)
The Guardian Legend: Secret Edition (Changes all the levels and is much more difficult than the original)
Pokemon Zeta (One of the best Pokemon games I've played; it was made in RPG Maker using Pokemon Essentials)
Mega Man X3: Zero Edition (Lets you play as Zero through the entire game, instead of only at certain points)
Super Mario Brothers X (A simultaneous co-op Super Mario game; you can also play as Link)
Super Mario Crossover (Play the original Super Mario Brothers as classic Nintendo characters)
That's all I can think of right this moment.
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