Platinum is my overall favourite, followed by Emerald and Silver as joint-second. Blue, despite being my first ever game, is third and tied with HG.
I just felt that everything in Platinum was...right. The story-line was upgraded from D/P and Cyrus had more in-depth characterisation, the Battle Frontier was incredible, and the battle system was sooo much better. (Whatever that lag thing was in D/P...way to ruin a game, developer.)
Emerald is my second-favourite because I adore Hoenn and I love that you had two evil Teams to go up against, and that they interacted with one another. I hope they bring something similar into B/W.
GSC...well, anybody who played GSC after RBY knows what I mean when I say they were fantabbytastic.
Blue...well, it was my first, but playing it again now with all of the extras added in just seems...oh, I dunno. You realise that there was a lot missing. Personally I see FR/LG as pretty much pointless except for importing Pokémon into my Diamond game. I've actually never played LG all of the way through :/
And HG...it's a brilliant remake of GSC, and the graphics and animations have blown me away, but the fact that I still enjoy playing Platinum instead means there's something missing from HGSS that I can't quite pick up on. I love the idea of Pokémon following you, and of the PokéWalker, though. Arceus always comes to Sainsburys with me now. :3