It is nearly impossible to keep this section organized, if you take into account the numbered book, the unnumbered ones, the crossovers, the comics, the standalone trilogies or mini-series (that sometimes share books between them), ebooks, parodies, young readers, short stories, guidebooks and standalones. I'll just do my best to keep some sense here.
Original Series
 Spectre - William Shatner
Dark Victory - William Shatner
Original Series Graphic Novels
Klingons - Blood Will Tell - Scott Tipton
Year Four - David Tischman
Year Four - The Enterprise Experiment - D.C. Fontana
Assignment: Earth - John Byrne
Mirror Images - Scott Tipton
Romulans - The Hollow Crown - John Byrne
Crew - John Byrne
Mission's End - Ty Templeton
Romulans - Pawns of War - John Byrne
Leonard McCoy, Frontier Doctor - John Byrne
Burden of Knowledge - Scott Tipton
Ruling in Hell - David Tipton
Infestation - Dan Abnett
The City on the Edge of Forever - Scott Tipton
Star Trek/Legion of Super-Heroes - Chris Roberson
Planet of the Apes: The Primate Directive - Scott Tipton
Year Five: Odyssey's End - Jackson Lanzing
Year Five: The Wine-Dark Deep - Jackson Lanzing
Year Five: Weaker Than Man - Jackson Lanzing
Year Five: Experience in Loss - Jackson Lanzing
The Next Generation
Encounter at Farpoint - David Gerrold
1. Ghost Ship - Diane Carey
2. The Peacekeepers - Gene Deweese
3. The Children of Hamlin - Carmen Carter
4. Survivors - Jean Lorrah
5. Strike Zone - Peter David
6. Power Hungry - Howard Weinstein
7. Masks - John Vornholt
8. The Captain's Honor - David and Daniel Dvorkin
9. A Call to Darkness - Michael Jan Friedman
10. A Rock and a Hard Place - Peter David
11. Gulliver's Fugitive - Keith Sharee
12. Doomsday World - Carter, David, Friedman, Greenberger
13. The Eyes of the Beholder - A. C. Crispin
14. Exiles - Howard Weinstein
15. Fortune's Light - Michael Jan Friedman
16. Contamination - John Vornholt
17. Boogeymen - Mel Gilden
18. Q-In-Law - Peter David
19. Perchance to Dream - Howard Weinstein
20. Spartacus - T. L. Mancour
21. Chains of Command - Bill McCay & Eloise Flood
22. Imbalance - V.E. Mitchell
23. War Drums - John Vornholt
24. Nightshade - Laurell K. Hamilton
25. Grounded - David Bischoff
26. The Romulan Prize - Simon Hawke
27. Guises of the Mind - Rebecca Neason
28. Here There be Dragons - John Peel
29. Sins of Commission - Susan Wright
30. Debtor's Planet - W.R. Thompson
31. Foreign Foes - Dave Galanter
32. Requiem - Micheal Jan Friedman & Kevin Ryan
33. Balance of Power - Dafydd ab Hugh
34. Blaze of Glory Simon Hawke
35. Romulan Stratagem - Robert Greenberger
36. Into the Nebula - Gene DeWeese
37. The Last Stand - Brad Ferguson
38. Dragon's Honour - Kij Johnson
39. Rogue Saucer - John Vornholt
40. Possession - J.M. Dillard
41. Invasion: The Soldiers of Fear - Dean Wesley Smith
42. Infiltrator - W.R. Thompson
43. A Fury Scorned - Pamela Sargent
44. The Death of Princes - John Peel
45. Intellivore - Diane Duane
46. To Storm Heaven - Esther M. Friesner
47. Q-Space - Greg Cox
48. Q-Zone - Greg Cox
49. Q-Strike - Greg Cox
50. Dyson Sphere - Charles R. Pellgrino
51. Infection - John Gregory Betancourt
52. Vectors - Dean Wesley Smith
53. Red Sector - Diane Carey
54. Quarantine - John Vornholt
55. Double or Nothing - Peter David
56. The First Virtue - Michael Jan Friedman
57. The Forgotten war - William R. Forstchen
58. Gemworld vol. 1 - John Vornholt
59. Gemworld vol. 2 - John Vornholt
60. Tooth and Claw - Dorrana Durgan
61. Diplomatic Implausibility - Keith DeCandido
62. Maximum Warp 1 - Dave Galanter
63. Maximum Warp 2 - Dave Galanter
64. Immortal Coil - Jeffrey Lang
The Q Continuum - Greg Cox
Metamorphosis - Jean Lorrah
Vendetta - Peter David
Reunion - Michael Jan Friedman
Unification - Jeri Taylor
Imzadi - Peter David
Relics - Michael Jan Friedman
The Devil's Heart - Carmen Carter
Descent - Diane Carey
Dark Mirror - Diane Duane
All Good Things - Michael Jan Friedman
Q-Squared - Peter David
Generations - J.M. Dillard
Crossover - Michael Jan Friedman
Kahless - Michael Jan Friedman
Ship of the Line - Diane Carey
The Best and the Brightest - Laurie Susan Wright
Planet X - Michael Jan Friedman
Imzadi II: Triangle - Peter David
I, Q - John de Lancie
The Valiant - Michael Jan Friedman
The Genesis Wave 1 - John Vornholt
The Genesis Wave 2 - John Vornholt
The Genesis Wave 3 - John Vornholt
Section 31: Rogue - Andy Mangels
A Hard Rain - Dean Wesley Smith
The Battle of Betazed - Charlotta Douglas
Genesis Force - John Vornholt
Do Comets Dream? - S.P. Somtow
Death in Winter - Michael Jan Friedman
Resistance - J.M. Dillard
Q & A - Keith DeCandido
Star Trek: TNG: The Skies the Limit - ed. Marco Palmieri
Before Dishonor - Peter David
Greater than the Sum - Christopher L. Bennett
Gods of Night - David Mack
Mere Mortals - David Mack
Lost Souls - David Mack
Losing the Peace - William Leisner
Paths of Disharmony - Dayton Ward
Spock vs. Q - Leonard Nimoy
Spock vs. Q: The Sequel - Cecelia Fannon
Indistinguishable from Magic - David A. McIntee
A Time to be Born - John Vornholt
A Time to Die - John Vornholt
A Time to Sow - Dayton Ward
A Time to Harvest - Dayton Ward
A Time to Love - Robert Greenberger
A Time to Hate - Robert Greenberger
A Time to Kill - David Mack
A Time to Heal - David Mack
A Time for War, A Time for Peace - Keith DeCandido
Starfleet Academy
1. Worf's First Adventure - Peter David
2. Line of Fire - Peter David
3. Survival - Peter David
4. Capture the Flag - John Vornholt
5. Atlantis Station - V.E. Mitchell
6. Mystery of the Missing Crew - Michael Jan Friedman
7. Secret of the Lizard People - Michale Jan Friedman
8. Starfall - Brad Strickland
9. Nova Command - Brad Strickland
10. Loyalties - Patricia Barnes-Svarney
11. Crossfire - John Vornholt
12. Breakaway - Bobbi J.G. Weiss
13. The Haunted Starship - Brad Ferguson
14. Deceptions - Bobbi J.G. Weiss
1. Voyager: Lifeline - Bobbi J.G. Weiss
2. Voyager: The Chance Factor - Diana G. Gallagher
3. Voyager: Quarantine - Patricia Barnes-Svarney
1. TOS: Crisi on Vulcan - Brad & Barbara Strickland
2. TOS: Aftershock - John Vornholt
3. TOS: Cadet Kirk - Diane Carey
Deep Space Nine
1. Emisary - J.M. Dillard
2. The Siege - Peter David
3. Bloodletter - K.W. Jeter
4. The Big Game - Sandy Schofield
5. Fallen Heroes - Dafydd ab Hugh
6. Betrayal - Lois Tilton
7. Warchild - Esther Friesner
8. Antimatter - John Vornholt
9. Proud Helios - Melissa Scott
10. Valhalla - Nathan Archer
11. Devil in the Sky
12. The Laertian Gamble
13. Station Rage
14. The Long Night
15. Objective Bajor
16. Invasion 3: Time's Enemy
17. The Heart of the Warrior - John Gregory Betancourt
18. Saratoga - Michael Jan Friedman
19. The Tempest - Susan Wright
20. Wrath of the Prophets - Peter David
21. Trial by Error
22. Vengeance - Dafydd ab Hugh
23. The 34th Rule - Armin Shimmerman
24. Rebels, Book 1: The Conquered - Dafydd ab Hugh
25. Rebels, Book 2: The Courageous - Dafydd ab Hug
26. Rebels, Book 3: The Liberated - Dafydd ab Hug
27. A Stitch in Time - Andrew J. Robinson
Not Numbered
Warped
The Search
The Way of the Warrior
Trials and Tribble-Ations
What You Leave Behind
The Lives of Dax
Star Trek: Deep Space Nine: Young Adult Series
1. The Star Ghost - Brad Strickland
2. Stowaways - Brad Strickland
3. Prisoners of Peace - John Peel
4. The Pet - Mel Gilden
5. Arcade - Diana G. Gallagher
6. Field Trip - John Peel
7. Gypsy World - Ted Pederson
8. Highest Score - Kem Antilles
9. Cardassian Imps - Mel Gilden
10. Space Camp - Ted Pedersen
11. Honor Bound: Day of Honor - Diana G. Gallagher
12. Trapped in Time - Ted Pedersen
Voyager
1. Caretaker - L.A. Graf
2. The Escape
3. Ragnarok
4. Violations
5. Incident at Arbuk
6. The Murdered Sun
7. Ghost of a Chance
8. Cybersong - S.N. Lewitt
9. Invasion
10. Final Fury
11. Bless the Beasts
Enterprise
TODO
Discovery
1. Desperate Hours - David Mack
2. Drastic Measures - Dayton Ward
3. Fear Itself - James Swallow
4. The Way to the Stars - Una McCormack
5. The Enterprise War - John Jackson Miller
6. Dead Endless - Dave Galanter
7. Die Standing - John Jackson Miller
8. Wonderlands - Una McCormack
Picard
Countdown #1-3 - Kirsten Beyer & Mike Johnson
1. The Last Best Hope - Una McCormack
2. The Dark Veil - James Swallow
3. Rogue Elements - John Jackson Miller
4. Second Self - Una McCormack
5. No Man's Land - Kirsten Beyer
Graphic Novels
The Q Conflict
Fool's Gold
Too Long a Sacrifice
Movie Novelizations
The Motion Picture
Star Trek II: The Wrath of Khan
Star Trek III: The Search for Spock - Vonda N. McIntyre
Star Trek IV: The Voyage Home - Vonda N. McIntyre
Star Trek V: Final Frontier
Star Trek VI: The Undiscovered Country
Star Trek: Generations
Star Trek: First Contact - J.M. Dillard
Star Trek: Insurection - J.M. Dillard
Star Trek: Nemesis - J.M. Dillard
Spinoff graphic novels
Star Trek: Countdown
Spock - Reflections
Star Trek: Nero
The Official Motion Picture Adaptation
Countdown to Darkness
Star Trek: Khan
New Adventures (Kelvin Timeline TOS characters)
Volume 1 - Mike Johnson
Volume 2 - Mike Johnson
Volume 3 - Mike Johnson
Volume 4 - Mike Johnson
Volume 5 - Mike Johnson
After Darkness - Mike Johnson
The Khitomer Conflict - Mike Johnson
Volume 8 - Mike Johnson
The Q Gambit - Mike Johnson
Volume 10 - Mike Johnson
Volume 11 - Mike Johnson
Volume 12 - Mike Johnson
Volume 13 - Mike Johnson
Boldly Go Volume 1 - Mike Johnson
Boldly Go Volume 2 - Mike Johnson
Boldly Go Volume 3 - Mike Johnson
Guides and Companion Books
The Nitpicker's Guide for Classic Trekkers - Phil Farrand
The Nitpicker's Guide for Next Generation Trekkers - Phil Farrand
The Nitpicker's Guide for Next Generation Trekkers II - Phil Farrand
The Worlds of the Federation - Shane Johnson
The Star Trek Encyclopedia - Michael Okuda & Denise Okuda & Debbie Mirek
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