So I've been developing this list of important or good (subjective, I know) Trek literature (books and comics, with references to the different TV series) by coming up with 32 different historical/series eras to put Trek literature into. It's based primarily on the Memory Beta Chronology.
It's still a rough draft, so there are quite a few mistakes, and I know it doesn't exactly fit the bill of what you were asking, but you did want something comprehensive! Hope this helps.
1. General
2. Myriad Universes
1968-2364
3. Earth’s Dark Era
4. Enterprise TV
5. Enterprise Books
6. Early Federation
7. Christopher Pike
8. Early Kirk
9. Vanguard
10. Star Trek Later Season One
11. Star Trek, Later Seasons
12. The Animated Series
13. Admiral Kirk
14. Kirk’s 2nd 5-Year Mission
15. The Original Films
16. Excelsior
17. Stargazer
18. Cardassian Occupation
2nd Half of the 24th Century (2364- )
19. Early TNG
20. Later TNG TV
21. Early DS9
22. Post-Series TNG
23. The Dominion War
24. Voyager
25. New Frontier
26. DS9 Relaunch
27. Mirror Universe
28. S.C.E.
29. A Time To…
30. Titan
31. Destiny
32. Voyager Relaunch
General
1. Strange New Worlds, 1-10
2. The Amazing Stories
3. The Captain’s Table
4. Tales from the Captain’s Table
5. Seven Deadly Sins
6. The Brave and the Bold
7. The Badlands
8. Day of Honor
9. Invasion!
10. Gateways
11. Star Trek: Special
12. The Modula Imperative
13. The Best of Gary Seven
Myriad Universes
14. Infinity’s Prism
15. Echoes and Refractions
16. Shattered Light
17. The Last Generation
18. Strangers in the Sky
19. Federation
20. Odyssey
21. Mirror Universe Trilogy
22. The Mirror Universe Saga
Earth’s Dark Era (1974-1996)
23. Assignment: Earth
24. The Rise and Fall of Khan Noonien Singh, Vol. 1-2
Enterprise TV (2151-2155)
25. Enterprise, Seasons 1-4
26. What Price Honor?
27. Daedalus
28. Daedalus’s Children
29. Last Full Measure
30. Rosetta
Enterprise Books (2155-2161)
31. The Good that Men Do
32. Kobayashi Maru
33. The Romulan War: Beneath the Raptor’s Wing
34. The Romulan War: To Brave the Storm
35. Starfleet: Year One
Early Federation
Christopher Pike (2228-2264)
36. Burning Dreams (2228-2267)
37. Crew
38. The Final Reflection
39. Final Frontier
40. Best Destiny
41. Collision Course
42. Vulcan’s Glory
43. The Early Voyages
44. Where Sea Meets Sky
45. Inception
Early Kirk (2264-2266)
46. Star Trek, Season One (2266-2267)
47. Constellations
48. The New Voyages
49. The New Voyages II
50. Mere Anarchy
51. Star Trek: The Original Series Omnibus
52. Romulans: Pawns of War
52. Enterprise: The First Adventure
53. My Brother’s Keeper: Republic
54. My Brother’s Keeper: Constitution
55. My Brother’s Keeper: Enterprise
56. The Janus Gate: Present Tense
57. The Janus Gate: Future Imperfect
58. The Janus Gate: Past Prologue
59. Errand of Vengeance: The Edge of the Sword
60. Errand of Vengeance: Killing Blow
61. Errand of Vengeance: River of Blood
Vanguard (2265-2267)
62. Vanguard: Distant Early Warning
63. Vanguard: Harbinger
64. Vanguard: Summon the Thunder
65. Vanguard: Reap the Whirlwind
66. Vanguard: Open Secrets
67. Vanguard: Precipice
68. Vanguard: Declassified
69. Vanguard: What Judgment Comes
Later ST Season One (2267)
70. Heart of the Sun
71. Web of the Romulans
72. Errand of Fury: Seeds of Rage
73. Errand of Fury: Demands of Honor
74. Errand of Fury: Sacrifices of War
75. Crucible: Provenance of Shadows
76. Crucible: The Fire and the Rose
77. Crucible: The Star to Every Wandering
78. Ishmael
79. The Disinherited
80. Invasion!: First Strike
81. The Case of the Colonist’s Corpse
82. The Galactic Whirlpool
83. Mission to Horatius
84. Twilight’s End
85. The Vulcan Academy Murders
86. The IDIC Epidemic
Star Trek, Later Seasons (2268-2269)
87. Star Trek, Season Two (2267-2268)
88. Star Trek, Season Three (2268-2269)
89. To Reign in Hell
90. Treaty’s Law
91. The Rings of Tautee
92. Uhura’s Song
93. Double, Double
94. How Much for Just the Planet?
95. Legacy
96. Section 31: Cloak
97. First Frontier
98. Mudd in Your Eye
99. Sanctuary
The Animated Series (2269-2270)
100. The Animated Series, Season 1-2
101. Faces of Fire
102. Assignment: Eternity
103. Planet of Judgment
104. World Without End
105. Perry’s Planet
106. The Three-Minute Universe
107. Renegade
108. The Great Starship Race
109. All of Me
110. The Patrian Transgression
111. Memory Prime
112. Prime Directive
113. The Tears of the Singers
114. Pawns and Symbols
115. The Price of the Phoenix
116. The Fate of the Phoenix
117. The Abode of Life
118. Chain of Attack
119. The Final Nexus
120. The Entropy Effect
121. Yesterday’s Son
122. Dreadnought!
123. Battlestations!
124. Troublesome Minds
125. Mission’s End
Admiral Kirk (2270-2272)
125. The Lost Years
126. Traitor Winds
127. A Flag Full of Stars
128. Recovery
129. Leonard McCoy, Frontier Doctor
Kirk’s 2nd 5-Year Mission (2273-2280)
1. Star Trek I
2. Untold Voyages
3. Ex Machina
4. The Kobayashi Maru
5. Home is the Hunter
6. Firestorm
7. Death Count
8. The Wounded Sky
9. Rihannsu: My Enemy, My Ally
10. Doctor’s Orders
11. Spock’s World
12. The Better Man
13. The Covenant of the Crown
14. Rihannsu: The Romulan Way
15. Rihannsu: Swordhunt
16. Rihannsu: Honor Blade
17. Rihannsu: The Empty Chair
18. Rules of Engagement
19. New Earth: Wagon Train to the Stars
20. New Earth: Belle Terre
21. New Earth: Rough Trails
22. New Earth: The Flaming Arrow
23. New Earth: Thin Air
24. New Earth: Challenger
25. Gateways: Chainmail
The Original Films (2281-2288)
26. The Pandora Principle
27. Dwellers in the Crucible
28. Time for Yesterday
29. Star Trek II-V
30. Unspoken Truth
31. In the Name of Honor
32. Probe
33. The Rift
34. The Best of Captain Kirk
35. The Best of Peter David
Excelsior (2289-2328)
36. Excelsior: Forged in Fire
37. Star Trek VI
38. Sarek
39. Mind Meld
40. Shadows on the Sun
41. The Last Roundup
42. The Captain’s Daughter
43. Vulcan’s Forge
44. The Sundered
45. Cast No Shadow
46. Serpents Among the Ruins
47. Terok Nor: Day of the Vipers
Stargazer (2327-2346)
48. Enter the Wolves
49. The Art of the Impossible
50. Stargazer: The Valiant
51. Stargazer: Gauntlet
52. Stargazer: Progenitor
53. Stargazer: Three
54. Stargazer: Oblivion
55. Stargazer: Enigma
56. Stargazer: Maker
57. Well of Souls
58. Vulcan’s Heart
Cardassian Occupation (2345-2367)
59. Terok Nor: Night of the Wolves
60. Deny Thy Father
61. The Buried Age
62. No Limits
63. Imzadi
64. Catalyst of Sorrows
65. Terok Nor: Dawn of the Eagles
Early TNG (2364-2368)
66. The Next Generation, Seasons 1-5
67. The Sky’s the Limit
68. The Best of Star Trek: TNG
69. Double Helix, 1-6
70. Survivors (2364)
71. Strike Zone (2365)
72. Metamorphosis (2365)
73. A Rock and a Hard Place (2366)
74. Gulliver’s Fugitives
75. Q-in-Law
76. Fortune’s Light
77. Contamination
78. Spartacus (2367)
79. Reunion (2367)
80. Perchance to Dream
81. The Star Lost
82. Vendetta (2367)
83. Chains of Command
84. The Forgotten War
85. The Last Stand (2368)
86. War Drums (2368)
87. Sins of Commission
88. The Romulan Prize (2368)
89. Intelligence Gathering
90. The Devil’s Heart
Later TNG TV (2369-2370)
91. The Next Generation, Seasons 6-7
92. The Best and the Brightest (2369-2372)
93. Here There Be Dragons (2369)
94. Guises of the Mind
95. The Death of Princes
96. The Best of the Borg (2369)
97. The Romulan Strategem
98. Foreign Foes
99. Requiem
100. Engines of Destiny (2370)
101. Blaze of Glory
102. Possession
103. Infiltrator
104. Into the Nebula
105. Q-Squared
106. Masks
107. Rogue Saucer
Early DS9 (2369-2373)
108. Deep Space Nine, Seasons 1-5
109. Prophecy and Change
110. The Never Ending Sacrifice
111. The Best of Deep Space Nine
112. The Siege
113. Klingon
114. The Landmark Crossover
115. Fallen Heroes
116. Antimatter
117. Devil in the Sky
118. Fool’s Gold
119. The Looking Glass War
120. Station Rage
121. The Long Night
122. Objective: Bajor
123. The 34th Rule
124. Legends of the Ferengi
125. Starfleet Academy, #1-19
126. Marvel DS9 #10-15
Post-Series TNG (2371-2373)
127. Ancient Blood (2371)
128. Crossover
129. Kahless
130. Do Comets Dream?
131. Perchance to Dream
132. Dujonian’s Hoard
133. Tooth and Claw
134. Generations
135. Ship of the Line (2372)
136. Slings and Arrows
137. Rogue
138. First Contact (2373)
The Dominion War (2373-2375)
139. Deep Space Nine, Seasons 6-7
140. Tales from the Dominion War
141. Behind Enemy Lines
142. Tunnel Through the Stars (2374)
143. Immortal Coil
144. Q-Continuum
145. The Gorn Crisis
146. Millennium, 1-3
147. Triangle: Imzadi II
148. The Battle of Betazed (2375)
149. Insurrection
150. Forgiveness
Voyager (2371-2377)
151. Voyager, Seasons 1-7
152. Distant Shores
153. Encounters with the Unknown
154. Mosaic
155. Pathways
156. The Escape (2371)
157. The Murdered Sun
158. The Black Shore (2373)
159. Echoes
160. Marooned
161. String Theory, 1-3 (2374)
162. Seven of Nine (2375)
163. Battle Lines
164. Shadow
165. Dark Matters, 1-3 (2376)
166. The Nanotech War (2377)
New Frontier (2373-2380)
167. New Frontier
168. Prometheans
169. Once Burned
170. Double Time
171. Double or Nothing
172. The Quiet Place
173. Dark Allies
174. Excalibur, 1-3
175. Cold Wars
176. Being Human
177. Gods Above
178. Stone and Anvil
179. After the Fall
180. Missing in Action
181. Turnaround
182. Treason
183. Blind Man’s Bluff
DS9 Relaunch (2375-2377)
184. The Left Hand of Destiny, 1-2
185. N-Vector
186. A Stitch in Time
187. The Lives of Dax (2376)
188. Avatar, 1-2
189. Section 31: Abyss
190. Gateways: Demons of Air and Darkness
191. Gateways: “Horn and Ivory”
192. Divided We Fall
193. Mission Gamma: Twilight
194. Mission Gamma: This Gray Spirit
195. Mission Gamma: Cathedral
196. Mission Gamma: Lesser Evil
197. Rising Son
198. Unity
199. Worlds of Deep Space Nine: Cardassia and Andor
200. Worlds of Deep Space Nine: Trill and Bajor
201. Worlds of Deep Space Nine: Feranginar and The Dominion
202. Warpath (2377)
203. Fearful Symmetry
204. The Soul Key
205. Reservoir Ferengi
Mirror Universe (2155-2181)
206. Mirror Images
207. The Sorrows of Empire
208. Glass Empires
209. Obsidian Alliances
210. Shards and Shadows
211. Rise Like Lions
S.C.E. (2376-2377)
212. Have Tech, Will Travel
213. Miracle Workers
214. Some Assembly Required
215. No Surrender
216. Foundations
217. Wildfire
218. Breakdowns
219. Aftermath
220. Grand Designs
221. Creative Couplings
222. Wounds
223. Out of the Cocoon
224. What’s Past
225. Turn the Page
226. Remembrance of Things Past
A Time To… (2375-2379)
227. I, Q
228. Gemworld
229. Diplomatic Implausibility (2376)
230. Maximum Warp, Book 1-2
231. A Good Day to Die
232. Honor Bound
233. Enemy Territory
234. A Burning House
235. The Genesis Wave, 1-3 (2376/2377)
236. The Genesis Force
237. Vulcan’s Soul, 1-3
238. A Time to be Born (2378)
239. A Time to Die
240. A Time to Sow
241. A Time to Harvest (2378/2379)
242. A Time to Love
243. A Time to Hate
244. A Time to Kill
245. A Time to Heal
246. A Time for War, A Time for Peace
247. Nemesis
Titan (2379-2380)
248. Death in Winter
249. Taking Wing
250. The Red King
251. Articles of the Federation
252. Orion’s Hounds
253. Resistance
254. Q & A
255. Before Dishonor
256. Sword of Damocles
257. Greater than the Sum
Destiny (2381-2382)
258. Destiny, 1-3
259. Over a Torrent Sea
260. Losing the Peace
261. A Singular Destiny
262. Rough Beasts of Empire
263. Watching the Clock
264. Synthesis
265. Zero Sum Game
266. Seize the Fire
267. Paths of Disharmony
268. The Struggle Within
269. Plagues of Night
270. Raise the Dawn
Voyager Relaunch (2378-2381)
271. Homecoming
272. The Farther Shore
273. Spirit Walk, 1-2
274. Full Circle
275. Unworthy
276. Children of the Storm