Planescape: Torment
Although Torment's gameplay is immensely satisfying at higher levels (especially for mages), and somewhat atypical for a D&D game, it cannot compete with the twisted depth and quality of the story. Wanting to soak in the story, the sights, sounds, and characters was more important to me as levelling up. I actually find Torment to be quite a bit more playable than the Buldur's Gate or Icewind Dale games.
TESIII: Morrowind
Poking at things, and hoping they die isn't that great. After some work, the combat gets a bit more complicated than that, but one can see how people might not enjoy it. Between the combat, running draining your fatigue, the probability factor, the gameplay isn't always amazing. The various stories that take place and the atmosphere of the game more than make up for it.
Fallout 2
Maybe I just couldn't build my character for shit, but most battles consisted of me constantly lading a save until the dice rolled in my favour. The various conversations, the many possibilities, and the rich dialogue all make the game highly enjoyable.
Deus Ex
Combat in Deus Ex wasn't exactly sophisticated. Neither was the hacking, or lockpicking. The exploration was quite nice, but not mind-blowing, by any means. However, Deus Ex did have some great dialogue, a compelling story, and my actions felt like they meant something whilst I was playing. Plus, a black Australian communist bartender in a dodgy Hong-Kong club.
Grim Fandango
I guess this goes for most point-and-click games, really.
Vampire The Masquerade: Bloodlines
For most of the reasons already mentioned. I greatly enjoyed some of the quest and characters, and the dialogue was usually very nice, especially for Malkavians. Very amusing.