Very, very, very tough call. I can narrow it down to five, but I can't pick one:
(in no particular order)
-Scribblenauts
-GTA: Chinatown Wars
-Kingdom Hearts
-Pokemon Heart Gold/Soul Silver
-Professor Layton and the Diabolical Box
Honourable mentions to:
-Fire Emblem: Shadow Dragon
-Phantasy Star Zero
-Call of Duty: Mobilised
-Retro Game Challenge
-Pokemon Platinum
-100 Classic Book Collection (just squeezes into 2009, in my opinion, as it wasn't released here in Australia until January)
My lists probably won't agree with everyone else's (especially the honourable mentions). But since the thread refers to what we enjoyed most personally.. well.. there it is.
There are many games, also, that I wanted to try but never got the time for, such as Devil Survivor and Mario & Luigi 3.