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Having read literally hundreds of Star Trek books, I'd have to say my favourites are the following:
Post-Nemesis/TNG Relaunch:
Articles of the Federation by Keith R.A. DeCandido
The Next Generation: Q & A by Keith R.A. DeCandido
The Next Generation: Greater than the Sum: Christipher L. Bennett
Star Trek: Destiny trilogy by David Mack
DS9 Relaunch:
A Stitch in Time by Andrew J. Robinson
Avatar: Books 1 and 2 by S.D. Perry
The Lives of Dax
The Left Hand of Destiny: Books 1 and 2 by J.G. Hertzler and Jeffrey Lang
Unity by S.D. Perry
Misc:
Star Trek: Terok Nor trilogy
Star Trek: Vanguard (Series, 5 books so far)
Star Trek: Myriad Universes (Series, 2 books so far, Infinity's Prism and Echoes and Refractions)
Note that the TNG and DS9 relaunches are considered canon by most and (along with other series, such as Star Trek: Titan) continue the story after Nemesis and "What You Leave Behind" DS9 finale.
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