1) Final Fantasy Tactics - I want to label it somewhere around 2 or 3, but I've probably spent enough time playing it to put up higher.
2) Xenogears - Disc 2 sucked, but the story presented by it was quite incredible and dramatic.
3&4) Metal Gear Solid 2&3 - I'm including both here because I don't know which is 3 and which is 4. They both have significant faults that make it hard for me to figure out which I like more.
5) Suikoden II - Probably the most emotionally compelling take on a war story I've ever experienced. And the ultra bad ending was one of the first games to make me cry.
6) Phoenix Wright: Trials and Tribulations - Fudge yeah!
7) Phoenix Wright: Ace Attorney - The original fudge yeah!
Final Fantasy VII - Screw you guys. Probably should be higher on my list, but it's been so long since I've played that I'm knocking it down a few points.
9) Xenosaga: Episode III - When I played it, I thought for a time that I was going to like it more than Xenogears. However, the hasty conclusion suffered similar faults as gears and was ultimately less dramatic and interesting.
10) FEAR - My favorite FPS for SHOOTAN. It's possible this will be surpassed with Resistance, but I need to give Resistance some more play before I make that decision.
Honorable mentions to Lunar: Silver Star Story Complete, Legend of Dragoon, Counter-Strike, Team Fortress 2, Neverwinter Nights 2: Mask of the Betrayer, Elder Scrolls III: Morrowind, and Baldur's Gate II. All of which have been favorite games at previous points and are not included somewhere on this list simply because of whim.