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There's a thing called PokeMMO which isn't affiliated with Nintendo, but they created a carbon-copy of Pokemon FireRed, only in an MMO world. It's pretty impressive, but the alpha stage is crap at the moment.
The Pokemon Company has yet to make any serious PC Pokemon Games as of yet, and it might not ever happen for a long time at the least. All of the ones you find are going to be fan-made. I don't know many fan games around that are done, so you might be stuck with hacks.