IMO, John M Ford's '
The Final Reflection' was outstanding. As a dedicated RPGer, I also liked how it tied in with the Klingon material for FASA's 'Star Trek' role-playing game (John M Ford also wrote that). Canon soon took both the Klingons and Federation history on a different path but, for me, this has always been THE Klingon book.
Also enjoyed his '
How Much For Just The Planet'. Lots of fun. Scottie's "duel" with one Klingon was absolutely priceless.
'
Trek To Madworld' brings back fond memories.
As does '
The Galactic Whirlpool'. I particularly liked the story-in-the-story ('
The MacMurray Encounter'), which would have made a great episode in the right hands.
Another book quickly overtaken by canon (de-canonized?) was '
Federation' by Judith and Garfield Reeves-Stevens. Written prior to 'First Contact' it crossed over between Zefrem Cochrane, TOS and TNG. Quite a different take to what was established in First Contact and, later, Enterprise, but still very
very good.
Diane Carey's '
The Great Starship Race' and '
Best Destiny' are also ones I like.
Lee Correy's '
Abode Of Life' is also very well done.
'
Strike Zone' (an early TNG novel) I give an honourable mention. Worf saves the day in a pivotal scene, then delivers one of the best throwaway lines in Trek history.
'
Q-In-Law', another early TNG novel. Q
and Lwaxana Troi on the Enterprise-D
at the same frackin' time 



. Once again, honourable mentions - Q gets some well-deserved comeuppance, and Worf gets more great lines.
Just about anything Diane Duane wrote for Trek I like - even if later canon changes have blown most of her work off the grid. '
Doctor's Orders', '
Spock's World', '
The Wounded Sky', '
The Romulan Way', '
My Enemy, My Ally' and TNG's '
Dark Mirror'* are all favourites of mine.
(* - Alternate 'Mirror Mirror' universe in the time of TNG, where the Terran Empire did NOT fall. ISS Enterprise-D, commanded by one Jean-Luc Picard, is a
scary ship - and its Deanna Troi is even scarier.)