Ahhhh, I can only pick 3? Hmmmm... This is a question that requires thought. Let me see. Here are my top 3:
Mass Effect: Yes, I mean 1 not 2. Some of you might be surprised by this choice, but let me explain. Yes, the second game was technically better, the controls were refined, the characters were deeper and the gameplay knocked several shades of fecal matter out of the first, but it lacked the soul the first game possessed. Seeing the Citadel for the first time, better storyline with an amazing villain, all the while blending great roleplaying elements. The first game left a much better first impression, it blew me away when I first played it. I'm also on my fourth playthrough, it's that good.
Metal Gear Solid - The Twin Snakes: Just like the original, but in my opinion better. I loved the way the game made you think outside the box (and in the case of that one codex number, on the box) and Psycho Mantis, for my money, was the most memorable boss battle I've ever played. Konami was on to a winner with the first installment of this great series.
Pokemon Heart Gold/Soul Silver: I don't think I've spent more time on any other game than this. At first glance it seems like a shallow turn based RPG, but when you dive into it, it's deeply involving and you really get a connection from the teams you raise yourself. This is a game that looks 2D, is 2D, but with more depth than many other RPGs out today. Plus it doesn't rely on great graphics to do it.