Many of these ones I'll mention have been in topics in the past:
SMBX is a fairly versatile Mario-game-making program, it's fun to just mess around in it from time to time, but if you want to put the work in your can make your own game with a custom world and such.
There's Pokemon Zeta and Omicron, which lets you run your own gym and has like all the Pokemon, not to mention MissingNo.
Pokemon Fusion is a play on that one generator where you grab two Pokemon and mix them together, but put into actual gameplay, I haven't played it myself however.
And Sonic Before the Sequel and After the Sequel are pretty good - they have some good music and custom textures which aren't really in a lot of Sonic edits, I believe because it isn't an edit but its own game but I don't remember.
