I liked FatherRob's post, so I'll do one like that.
ENT:
Nada. The relaunch had promise, but Romulan War was seriously bleh.
TOS:
Ex Machina (you may notice a lot of Christopher on this list...)
Federation (perhaps the best of the zero-continuity TrekLit era)
The Pandora Principle (great backstory for Saavik)
I haven't read Crucible yet, so so far, that's it; not a huge TOS fan
VGD:
All of it, but especially Reap The Whirlwind.
Lost Era:
Serpents Among The Ruins (one of my favorite endings of a novel ever)
The Art Of The Impossible (amazing worldbuilding)
The Buried Age (the book that got me back into TrekLit)
TNG pre-Nemesis:
Vendetta
Imzadi
Q-Squared (all of PAD's early work was great, but these were the best)
TNG Relaunch / Wider Federation:
Articles Of The Federation (KRAD at his best)
***DESTINY*** (too awesome to even explain)
Losing The Peace (made me like Crusher, amazingly enough)
DS9:
The Siege (amazingly good for an early novel)
The Lives Of Dax (greater than the sum of its parts)
A Stitch In Time (an incredible character study)
Plus, really, the whole relaunch, but especially:
Avatar (still stunningly well done)
Twilight (DRG3's best that I've read so far; powerful themes)
The Never-Ending Sacrifice (amazing this was ever published, but I'm happy it was)
VOY:
Captain's Table: Fire Ship (best character study on Janeway I've seen)
Myriad Universes: Places Of Exile (what Voyager should've been)
And of course all of Beyer's relaunch-2
NF:
Captain's Table: Once Burned (beautiful little tragedy)
Stone & Anvil (every great aspect of this series at its best)
SCE:
Wildfire (didn't like much of the rest, but this story is insanely powerful; a masterpiece)
Titan:
Orion's Hounds (finally got the series on the right track after the weirdly unfocused first two)
Sword of Damocles (one of the most unique writers in TrekLit's history, worth it just for that)
Over A Torrent Sea (so many great ideas)
MU:
The Sorrows Of Empire, expanded (so epic. sooooo epic.)