Let me help:
The Rise of the Federation is actually the second era in the Enterprise relaunch, before that was a series that covered the Romular War and the events leading up to it.
Books:
- Last Full Measure by Michael A. Martin & Andy Mangels (Relaunch prequel set during Season 3)
- The Good That Men Do by MAM & AM
- Kobayashi Maru by MAM & AM
- The Romulan War: Beneath The Raptor's Wing by MAM
- TRW: To Brave the Storm
I'm pretty sure there have been some other TOS books that tie into the Novelverse, but I'm not sure which they are
CLB has also written two more books that take place in the era. The first one was part of the TOS Mere Anarchy e-book miniseries, which followed the TOS crew's interactions with a planet throughout their history.
Mere Anarchy:
- Things Fall Apart by Dayton Ward & Kevin Dilmore (pre-TOS)
- The Center Cannot Hold by Mike W. Barr (during TOS)
- Shadows of the Indignant by Dave Galanter (between TOS and The Motion Picture)
- The Darkness Drops Again By CLB (between TMP and The Wrath of Khan)
- The Blood Dimmed Tide by Howard Weinstein (between The Final Frontier and The Undiscovered Country)
- It's Hour Come Round by Margaret Wander Bonanno (after the Generations prolouge)
Bennet's second TMP era story as also part of the 24the century Department of Temporal Investigations series I'll cover later.
Vulcan's Heart is actually part of a series informally known as the Vulcan's Noun series all of which are written by Sherman and Shwatz.
Books:
- Vulcan's Forge
- Vulcan's Heart
After the first two books the series becomes the Vulcan's Soul trilogy, which takes place after the Dominion War
Vulcan's Soul:
- Exodus
- Exiles
- Epiphany
Along with the main novels there were also a crossover with the 23rd century SCE crew that acted as a prequel for the series.
The series also had an e-book novella follow up focused on the TOS characters
After that, Ward & Dilmore and Mack launched a spinoff series focused on two starship crews after the end of Vanguard. The series flips back and forth with each book, with Mack writing one and Wardimore covering the other.
Seekers:
- Second Nature by Mack
- Point of Divergence by Wardimore
- Long Shot by Mack
- All That's Left by Waridmore
The Sorrows of Empire was actually part of a bigger MU saga, the first two books featured three short novellas.
Mirror Universe:
- Age of the Empress (Enterprise) by Wardimore, story by Mike Sussman (the writer of the Ent. Mirror Universe episodes)
- The Sorrow of Empire novella version (TOS) by Mack
- The Worst of Both Worlds (TNG) by Greg Cox
- The Mirror Scaled Serpent (Voy) by KRAD
- Cutting Ties (New Frontier) by Peter David
- Saturn's Children (DS9) by Sarah Shaw (actually an pseudonym for David Mack)
These were followed up by a short story collection that covered the other series not covered by the first two, and featured sequels to the some of the novellas.
- Ill Winds (April-era TOS) by Wardimore
- The Greater Good (Piker-era TOS) by MWB
- The Black Flag (Van) by James Swallow
- The Traitor (STG) by Michael Jan Friedman
- The Sacred Chalice (The Worst of Both Worlds sequel) by Rudy Josephs
- Bitter Fruit (The Mirror Scaled Serpent sequel) by Susan Wright
- Family Matters (Klingon Empire) by KRAD
- Homecoming (NF) by PD
- A Terrible Beauty (Keiko Ishikawa/O'Brien) by Jim Johnson
- Empathy (Titan) by CLB
- For Want of a Nail (K'Ehleyr & Barclay) by DM
- Following Shards and Shadow the expanded version The Sorrows of Empire was released.
- Rise Like Lions by DM tied up most of the storylines introduced by the MU novellas and short stories and also set up future stories.
There were several more TLE novels you missed, and Day of the Vipers is the first book in a trilogy. While it was mainly marked as TNG, TBA is also a TLE novel.
- The Sundered by MAM & AM
- Well of Souls by Ilsa J. Bick
- Deny Thy Father by Jeff Mariotte
- Catalyst of Sorrows by MWB
- Terok Nor trilogy
- Day of the Vipers by James Swallow
- Night of the Wolves by SD Perry & Britta Dennison
- Dawn of the Eagles by SDP & BD
- One Constant Star by DRGIII
You missed the Stargazer series, which covers the beginnings of Picard's captaincy of the USS Stargazer. All of the SGZ stories are written by Michael Jan Friedman.
- TNG: Reunion (TNG series era book that introduced the characters who would go on to star in SGZ.
- TNG: Requiem (another series era novel that features the SGZ crew in the prologue)
- The Valiant (marked as a TNG book, but actually the first Stargazer novel)
- Double Helix/TNG: The First Virture (Stargazer story that served as a prolouge for the Double Helix miniseries)
- Gauntlet (Fist book actually marked as SGZ)
- Progenitor
- Three
- Oblivion
- Enigma
- Maker
The Tales of The Domion War, Tales from the Captain's Table anthologies also feature SGZ short stories.
There are several more TNG books from that era that I know tie into the novelverse. The first one is the second book in the Gateways miniseries, which saw each of the then current series deal with the Iconian Gateways.
- Gateways (The crossover featured DS9 Relaunch and NF novels):
- One Small Step (TOS) by Susan Wright
- Chainmail (Challenger) by Diane Carey (This is the second book of the Challenger series, which was itself a spin-off from the TOS miniseries New Earth. I believe it was intended to be an ongoing series, but never made it past this book)
- Doors Into Chaos (TNG) by Robert Greenberger
- Demons of Air and Darkness (DS9 Relaunch)
- No Man's Land (Voy) by Christie Golden
- Cold Wars (NF) by PD
- What Lay Beyond by all of the above (Each book ended with a cliffhanger that was resolved in a novella featured here)
Around this time we also got a Section 31 minsieries with took a similar approach with the title agency.
- Cloak (TOS) by SDP
- Rogue (TNG) by MAM & AM (introduces a character who would go on to appear in DS9, and be a major character in TTN)
- Abyss (DS9 Relaunch) by David Weddle (a regular writer on the DS9 TV series, Battlestar Galactica and others) & Jeffrey Lang
- Shadow (Voy) by Dean Wesley Smith & Kristine Kathryn Rusch
- Gemworld Bk 1 & 2 by John Vornholt(this duology features Melora Pazlar, who was introduced in a DS9 episode and then became a main character on Titan.)
- Maximum War Bk 1 & 2 by Dave Galanter & Greg Brodeur (features a character who later appeared in the DS9 Relaunch, and I believe it's events have been referred to in later books)
- Q Continuum trilogy by GC (I believe we have gotten references to these)
- Q-Space
- Q-Zone
- Q-Strike
These were the last three books in a nine book series leading into the events of Nemesis.
- Be Born by JV
- Die by JV
- Sow by Wardimore
- Harvest by Wardimore
- Love by RG
- Hate by RG
- Kill by DM
- Heal by DM
- For War, For Peace by KRAD
You also missed a bunch of TNG novels set between Nemesis & Destiny
- Death in Winter by MJF
- Resistance by JM Dillard
- Q & A by KRAD
- Before Dishnor by PD
- Greater than the Sum by CLB
Destiny is not just a TNG trilogy, it is a massive crossover featuring characters from TNG, DS9, Titan, and Enterprise. It was a huge game changer for the entire novelverse from that point on.
- Losing the Peace by William Leisner is TNG's follow up on Destiny
The Typhon Pact Miniseries comes between LTP and TCE. While the books were all marked as TP, they were pretty much just books in their respective series that deal the newly introduced group, The Typhon Pact.
- A Singular Destiny by KRAD was a standalone novel focused on a new character that dealt with the post Destiny universe, and set up the Typhon Pact.
- TP: Paths of Disharmony by DW
- Indistinguishable from Magic by David McIntee was a standalone TNG novel focused on Geordi La Forge
- TP: The Struggle Within by CLB (e-book novella)
- The Stuff of Dreams by JS (e-book novella)
The Fall was another miniseries similar to Typhon Pact with each book focusing on a specific group of characters following a big event in the first book. The Poisoned Chalice was not a TNG book, it was the series Titan entry.
- Crimson Shadow by Una McCormack
- Peaceable Kingdoms by DW
You missed the first two Titan novels, a two parter by MAM & AM
- The Sword of Damocles by Geoffrey Thorn comes between Orion's Hounds and Destiny.
- Over a Torrent Sea by CLB comes between Destiny and Synthesis
Peaceable Kingdoms is TNG not TTN
- Absent Enemies by John Jackson Miler (e-book novella)
The Worlds of DS9 miniseries followed Unity. Each book contain two novellas that focused on a specific group of characters and was based around a planet or group.
- Cardassia: The Lotus Flower by UM
- Andor: Paradigm by Heather Jarman
- Trill: Unjoined by MAM &AM
- Bajor: Fragments & Omens by J. Noah Kym (Kym's bio is rather vague, so some have theories this is a psuedonym)
- Ferenginar: Satisfaction is Not Guaranteed by KRAD
- The Dominion: Olympus Descending by DRGIII
- Warpath by DM
- Fearful Symmetry by Olivia Woods
- The Soul Key by OW (this and FS both tie into the Mirror Universe saga)
- TP: Zero Sum Game by DM takes place here
The three books listed above weren't specially marked as a trilogy. RBOE was a stand alone entry in the TP series, and the other two were a duology that followed some of it's events, and also tied together events from some of the other TP novels.
- TF: Revelation and Dust by DRG III specifically follows up on the events of the three TP books.
I haven't read it yet myself, but I'm thinking The Crimson Shadow would probably be best read with the other The Fall books
- If you include Mosaic you should probably include Taylor's follow up Pathways. It's worth noting these books are not part of the novelverse since they were contradicted by later canon.
- I believe the Sting Theory trilogy, set between Seasons either 4 & 5 is specifically referred to in the Relaunch.
- Cohesion by Jeffrey Lang
- Fusion by Kristing "NYTBSMFin'" Beyer (not her official credit, but it is our affectionate nickname for her here)
- Evolution by Heather Jarman
Following Stone and Anvil the NF series jumped to the post-nemesis era and continued
- After the Fall
- Missing in Action
- Turnaround (IDW Comics miniseries, ties into MU:NF stories, but also contradicts the non-NF MU stories)
- Treason
- Blind Man's Bluff
- The Return (3 part e-book miniseries)
The two part Wildfire storyline are the 23rd and 24th novellas in the SCE e-book novella series. Following the 66th novella, the series changed it's title to Corps of Engineers, and stopped numbering the books. There were 8 more novellas following the name change.
The first 66 novellas were collected into paperback omnibuses.
- Have Tech Will Travel
- Miracle Workers
- Some Assembly Required
- No Surrender
- Foundations (introduces the 23 SCE crew on the USS Lovel, these characters were also featured in Vanguard)
- Wildfire
- Breakdowns
- Aftermath (at this point the paperback collections changed the series title to Corps of Engineers, even though the original novellas were still SCE)
AoTF is a stand along story focused on the first year of a new UFP Presidents time in office between Nemesis and Destiny.
Already covered this one earlier.