This is a very tough one for me. I loved Pokemon HG/SS because it brought back a lot of nostalgia for me. On the other hand, I also loved Super Mario Galaxy 2. However, I'm going to have to go with HG/SS on this one. Like I said, the feeling of nostalgia really takes the cake for me. I've often called the original Gold and Silver versions "The best Pokemon games of all time." They're also my favorites -- and with good reason, too. Everything about these games was superb. From the storyline, to the region, right down to the music, everything in the old version seemed to click with me. When HG/SS came out, I played the Heart Gold. Boy, was I impressed. Somehow, Nintendo found a way to take a masterpiece, and refurbish it to the point of making it seem new again. Like the old games, everything clicked. The old storyline was there, and there were even some new things to do in it. The graphics were revamped and looked absolutely superb for a Nintendo DS game. Add in the fact that you had added Pokemon from the other games, and you have yourself a hell of a game.
Super Mario Galaxy is a close second, but Pokemon HG/SS take the cake for me.