Okay, here we go....
S.C.E.
#1: The Belly of the Beast by Dean Wesley Smith: Features Montgomery Scott (TOS) and the Enterprise-E, in particular Jean-Luc Picard, Geordi La Forge, and Christine Vale (TNG).
#2: Fatal Error by Keith R.A. DeCandido: Features La Forge (TNG).
#3: Hard Crash by Christie Golden: Features the Enterprise-E, in particular Picard and La Forge (TNG).
#4: Interphase Book 1 by Dayton Ward & Kevin Dilmore: Features William Ross (DS9). Also features Scotty and is a sequel to "The Tholian Web" (TOS).
#5: Interphase Book 2 by Dayton Ward & Kevin Dilmore: Features Ross (DS9). Also features Scotty and McCoy and is a sequel to "The Tholian Web" (TOS).
#6: Cold Fusion by Keith R.A. DeCandido: Features Scotty (TOS). Also features Nog, Kira Nerys, and Empok Nor, and takes place between Avatar Book 2 and Section 31: Abyss (DS9).
#7: Invincible Book 1 by David Mack & Keith R.A. DeCandido: Features Scotty (TOS).
#10: Here There Be Monsters by Keith R.A. DeCandido: Crosses over with the Gateways miniseries, includes mentions of Scotty and the TNG and NF crews.
#12: Some Assembly Required Scott Ciencin & Dan Jolley: Features Scotty (TOS).
#13: No Surrender by Jeff Mariotte: Features Scotty (TOS). Ties into the episode "Too Short a Season" (TNG).
#14: Caveat Emptor by Ian Edginton & Mike Collins: Features Grand Nagus Rom (DS9). Also features Scotty and ties into the episode "Return of the Archons" (TOS).
#15: Past Life by Robert Greenberger: Features Ross (DS9) and the Evora from Insurrection (TNG).
#16: Oaths by Glenn Hauman: Takes place on Sherman's Planet from "The Trouble with Tribbles" (TOS).
#17: Foundations Book 1 by Dayton Ward & Kevin Dilmore: Features Scotty (TOS). Flashback to the U.S.S. Lovell (VGD).
#18: Foundations Book 2 by Dayton Ward & Kevin Dilmore: Features Scotty and is a sequel to "Return of the Archons" (TOS). Flashback to the U.S.S. Lovell (VGD).
#19: Foundations Book 3 by Dayton Ward & Kevin Dilmore: Features Scotty and is a sequel to "By Any Other Name" (TOS).
#20: Enigma Ship by J. Steven York & Christina F. York: Features Reginald Barclay (TNG/VOY) and Scotty (TOS).
#21: War Stories Book 1 by Keith R.A. DeCandido: Flashbacks to the Dominion War, and features Ross, Benjamin Sisko, Miles O'Brien, and Martok (DS9). Also features Janice Kerasus (TOS).
#22: War Stories Book 2 by Keith R.A. DeCandido: Flashback to the Dominion War (DS9).
#23: Wildfire Book 1 by David Mack: Features Lian T'su (TNG).
#25: Home Fires by Dayton Ward & Kevin Dilmore: Features Ross (DS9).
#28: Breakdowns by Keith R.A. DeCandido: Features Scotty (TOS) and Ross (DS9).
#29: Aftermath by Christopher L. Bennett: Features Scotty (TOS), O'Brien, Ross, and Keiko O'Brien (DS9).
#30: Ishtar Rising Book 1 by Michael A. Martin & Andy Mangels: Features Scotty (TOS).
#32: Buying Time by Robert Greenberger: Features Brunt (DS9).
#33: Collective Hindsight Book 1 by Aaron Rosenberg: Flashback to the Dominion War (DS9).
#37: Ring Around the Sky by Allyn Gibson: Ties into the Invasion! miniseries.
#40: Failsafe by David Mack: Features Scotty (TOS).
#43: Paradise Interrupted by John S. Drew: Features Scotty (TOS).
#44: Where Time Stands Still by Dayton Ward & Kevin Dilmore: Flashback to the Lovell (VGD). Sequel to "The Time Trap" (TAS).
#45: The Art of the Deal by Glenn Greenberg: Features the Enterprise-E, in particular Picard and Vale (TNG).
#50: Malefictorum by Terri Osborne: Features Deep Space 9, in particular Quark, Ro, Kira, and Treir, and also Luaran (DS9). Makes use of the mobile emitter (VOY) and VR technology from "Interface" (TNG).
#51: Lost Time by Ilsa J. Bick: Features Deep Space 9, in particular Kira, Nog, Elias Vaughn, and Ezri Dax, as well as alternate-reality versions of various folks (DS9).
#53: Fables of the Prime Directive by Cory Rushton: Features a Vorta (DS9).
#54: Security by Keith R.A. DeCandido: Features Vale (TNG) and Kira (DS9).
#55-56: Wounds Books 1-2 by Ilsa J. Bick: Features Julian Bashir (DS9).
#57: Out of the Cocoon by William Leisner: Sequel to "Up the Long Ladder," and features Brenna and Grainger (TNG).
#60: The Cleanup by Robert T. Jeschonek: Features elements from the Dominion War (DS9).
#61: Progress by Terri Osborne: Features Katherine Pulaski and is a sequel to "Pen Pals" (TNG).
#62: The Future Begins by Steve Mollmann & Michael Schuster: Features Scotty (TOS), La Forge (TNG), Ross (DS9), Alynna Nechayev (TNG/DS9), and the Lefler family (NF). Flashback to the Dominion War (DS9). Ties into the Excalibur trilogy (NF).
#63: Echoes of Coventry by Richard C. White: Features Marta Batanides from "Tapestry" (TNG). Flashback to the Dominion War (DS9).
#64: Distant Early Warning by Dayton Ward & Kevin Dilmore: Flashback to the Lovell, and is a prequel to the Vanguard series.
#65: 10 is Better than 01 by Heather Jarman: Flashback to the Dominion War (DS9). Features Orfil Quinteros from "11001001" (TNG).
#66: Many Splendors by Keith R.A. DeCandido: Features the Enterprise-D, in particular La Forge, Picard, William Riker, Wesley Crusher, and many many many others (TNG). Ties into several TNG episodes.
Corps of Engineers
Troubleshooting by Robert Greenberger: Features Ross (DS9).
The Light by Jeff D. Jacques: Features a downed Borg cube (TNG/VOY).
The Art of the Comeback by Glenn Greenberg: Features Scotty (TOS).
Signs from Heaven by Phaedra M. Weldon: Features Scotty and is a sequel to "The Cloud Minders" (TOS).
Ghost by Ilsa J. Bick: Features Scotty and McCoy (TOS).
Remembrance of Things Past Book 1 by Terri Osborne: Features Picard, Vale, and Data (TNG).
Remembrance of Things Past Book 2 by Terri Osborne: Features Picard, Vale, and Data and ties into the episode "Pen Pals" (TNG).