Well, I really enjoyed the plots of X-Wing: Tie Fighter and especially X-Wing: Alliance. They had a surprisingly deep stories which slowly unfolded and really pulled you into the universe. There are some thrilling sequences which are cleverly foreshadowed in earlier missions, and it's great that particularly in XWA there are times when you think the mission is over only to realize that there are yet things to be done as the stakes get higher. Character development in XWA was well done, and the characters matured and changed as the story progressed instead of staying the same, which was a nice touch.

Fallout 1 & 2 had great stories as well. Although the games themselves are partly open-ended with the way that you can decide the fate of several organizations and people, the main storylines were thrilling with quite a few plot twists (there are some that you'd never expect to happen, which is a great plus) and well-written characters. The subject matter is appropriately dark and mature, and the story helps pull you into the world the games take place in.