It depends on what you are looking for as a fangame.
With fakemons, i would definetely recommand Pokemon Uranium (RMXP), which maybe is the best fakemon game, and maybe even the sole. Quite refreshing. There also are the romhacks from Baro, Pokemon Quartz and its sequel but they are quite old now.
For a different region and story of the official games, but with no fakemons, the only good one i know is Glazed.
If you're looking for some challenge and roster improvements only (like the very same game as the original, but harder and with all the pokemons), there are Expert Emerald for the third gen and Complex Crystal for the second.
You should definetely give a try to the Twitch Red Anniversary romhack when it's out too.
For remakes that takes liberties, Liquid Crystal is a very very good one, especially if you liked the original GSC. And you have to play Pokemon Adventures Red Chapter (there also are demos for Green/Blue/Yellow chapters i think, but i didn't try them).
I heard many good things about LightPlatinum, but unfortunately have never been able to patch it or find the game already patched. Maybe if someone could send me a PM there...