Why are people judging the games instead of the generations? XD This is a poll about the generations, not the games.
Point in case: I'm not at all impressed with many of the Pokemon of G/S/C/HG/SS, but I love HeartGold to death. I never played the original Gold or even Crystal, but HeartGold's storyline is epic and I had so much fun playing the game that I'm seriously not surprised so many people are fond of G/S/C. But Pokemon-wise, a lot of them are (or were) crappy, until the 4th gen came along and made it all better.
Anyways, I voted for the III and IV generations. To me, the first generation was the third generation, XD. But I don't really have a favourite, all I know is that I love the Pokemon of Hoenn and Sinnoh better than those of Kanto and Johto, but that's that. Mostly I loved III and IV for its Grass types and their great variety (let's face it, the Grass types in Kanto and Johto are mostly ****; the Kanto Grass/Poison types are all outclassed by Roserade big time, and every Grass in Johto except Meganium and Celebi is rather weak).
But for the record, the best games (imo) are: Heart Gold > Platinum > Emerald.