Well my new favorite is Diamond. There's just so much to do.
But for the longest time my favorite was Silver. It was the first Pokemon I played, and it was a big game. I mean in Red/Blue/Yellow, all you had was Kanto and 8 badges. In Silver you started out in Johto and then you could go to Kanto. So you had 16 badges to get instead of just 8. There were also more Pokemon to catch and raise.
On Silver I ended up filling the Pokedex except for Mew and Celebi, and I put in a good 400 or so hours.
Diamond is getting there. I think I've got something like 260 Pokemon and 100 hours.