Ruby, Platinum, SoulSilver, and White 2 all have to be my favorite versions to date.
─ Ruby was the first Pokémon game I got, and I've played it more times than I can remember.
─ Platinum, to me, was near perfect. It had a fantastic level curb, a nice variety of Pokémon, and it managed to correct the things Diamond and Pearl did wrong.
─ SoulSilver (and HeartGold) are GameFreak's current best remakes and they're just a lot of fun. You get to enjoy everything from the originals and then some.
─ White 2 I just recently finished ─ well, I beat the Elite 4 anyway ─ and it was an all around great game. A big improvement over Black and White in my opinion.