My personal fav is Gold, that was the first one that I played.
I picked FireRed, for that is the only game that I've actually takin' the time to beat. . .
I'm staying loyal to my first game, Sapphire. Really, I love it because it pretty much lead me into the world of pokemon.
My vote goes to GSC, since that was pkmn's high point, IMO. After first gen, they added so many nice changes, the new pkmn were good enough, really. The day/night system is back in DP, but for whatever reason never made it to RSE. Besides, I was just a Crystal version fanatic back in the day...really, third gen somewhat ruined everything, minus a few really nice pkmn (i.e. Whiscash+'vanha)...