1. Arcanum: Of Steamworks & Magick Obscura
2. Planescape: Torment
Someone needs to emulate this kind of engine in a new game.
4. The Spirit Engine 2
Cool combat, cool story, neat way to vary the story and mechanics upon replaying.
5. Mount & Blade
I only played the demo, so I couldn't tell how deep the game got, but I loved the ugliness of combat and the sense of doom that must have hung over people's heads when charging into combat back before you could reliably pick someone off at range. That, and it's fun to shoot people with arrows, too.
6. Star Wars: The Old Republic
The dialog, maybe? Every MMO is different de-facto, otherwise someone gets sued. In a way Bioware tried new things, having companions and strong solo content, but they played it very safe in other ways. Makes for a weird mix. I'm not sure how they're doing financially speaking, but recent behavior suggests a shortfall.