Has to be "I, Jedi" - seeing the Star Wars Universe from the perspective of someone like Corran Horn (trainee Jedi, yet hardened pilot and former CorSec Officer) gives a lot of life to the whole thing. Aside from offering a lot of insight into the Jedi in their post-ROTJ days, I think he has some of the strongest character development found in any single book.
Beyond that, "Traitor" in the NJO series is just a superb book. The Unifying Force is introduced here in a staggering way, and it offers a wonderfully-contrasting approach to the whole Jedi/Sith problem, Jacen Solo being trained as a mixture of both (although his teacher, Vergere, is only spoken of as Sith about 10-12 books down the line, and even then not directly admitted as such) - essentially pushing the reader towards the conclusion that the Light/Dark Dichotomy is complete nonsense when taken against the Force as a whole. Really, really fantastic book. Very philosophical, and insightful.