My main series favorite was Yellow, but my favorite one on the side games has to be either Mystery Dungeon Time or Gates to Infinity. I really like the gameplay and the storyline. Gates to Infinity had me bawling for two hours straight after I beat it. Love that game :D
I'm playing Emerald right now. I don't know any of the new Pokemon, but I have a chicken and some beast. I have always liked Mew though. Mewtwo can go kick rocks. Mew is the shizz.