Pokemon Silver/Gold, then Black/White as a close second in my opinion.
It's always the third game of every generation.
Yellow was great, Game Freak had the time to work on the sprites. Emerald and Crystal had better storylines than Ruby/Sapphire and Gold/Silver. I never played Platinum, so I can't say anything bad about it.
Red and Blue could have been so much better. If Game Freak wasn't rushed, there's so many things that could have been fixed. We even could have had a second rival.
But the glitches were fun.
I would have to say that the second generation of Pokemon games {G/S/C and the remakes} were the best out of all of them. Not only did they have a new region in Johto to explore, but you could also go back into the Kanto region and fight the gym leaders there, which added a whole bunch of replayability with the games. Also, 251 Pokemon was the right number for Pokemon to catch, plenty enough so that every type had some representation, but reasonable enough for most people to keep track of, considering that adding 100+ or so Pokemon every generation after this generation would be too repeative.
Also, they managed to correct a lot of the quirks and problems from the first generation, along with adding an experience bar and the first generation where your Pokemon can hold certain items, which makes the battles more strategic and reduce the emphsis on luck. I could go on and on about the improvements, but there are too many to mention that most people already know of.
Just stop worrying, and love the bomb.
