Can I say 2? My favorite and my second favorite? NO? To bad.
My second favorite game is persona 4. The characters are fantastic, while still being realistic, the battle system is superb, as is the story. The also has.. I don't know, its hard to describe. I guess the best way to describe it is that it has a lot of heart. Also, the good ending (The first one I got) Made me cry like a little *****. It's not sad or anything, but if you had played the game and then saw it you'd understand why.
My favorite is Valkyria Chronicles and the simplest way to put it is that to me, this game is perfection. The gameplay, soundtrack, characters (Though they aren't as good as P4's), graphics, story, and rpg elements all blend together beautifully.