The main plot from Jedi Knight is still possibly one of my favorite EU stories out there. And of course the game was amazingly cool for its time. Mysteries of the Sith was also lots of fun.
Jedi Outcast completely blew me away with its visuals and the gameplay mechanics of force powers and lightsaber combat. As captainsolo says, it remains the pinnacle of lightsaber and force use in the video game world.
Loved those two games.