Although I've never played the second generation competitively, it's probably my favorite due to nostalgia. Too many awesome Pokemon were ceated in that generation (Scizor, Meganium, Tyranitar, Elekid, Typhlosion, Steelix).
Everyone's always pursuaded to like Johto the most because 'you got to go back to Kanto'.. but I don't see why this was so ground breaking, GSC was easily the worst. It did bring quite a bit to the table, but this was all improved drastically in the next games. Johto was actually a rather small and not overly exciting place, the story was so much better in RSE. Johto is small and I think every generation bar possibly DPP has better Pokémon within it.
I voted RSE, by the way. DPP has a better battle system and further breeding upgrades etc, but Hoenn wins out at everything else. (Although I haven't played Platinum yet, I could like that more than Emerald, but I kind of doubt I will).
I find that, for the most part, the generation people like best is the one they "really" started with - the first one they really invested time in.
Me, I played Red and Blue religiously as a kid, so I like those the best.