I expect this to get long as I am still playing the Star Wars The Old Republic game and I can’t walk a few steps without running into references. This isn’t surprising as its a follow up to the Knights of the Old Republic series which itself was based on the Tales of the Jedi comic books and graphic novels.
Playing as Jedi Consular and Smuggler so far, this is what I have found.
Possible Acknowledgement: The Wanderlust freighter that helps Force Sensitives flee Balmorra is co-owned by Rostoni. This may (likely) be a nod to Sue Rostoni, former executive editor and fiction and comic editor at Lucas Licensing.
The Noetikons reference Jedi Masters from the comic books. These include Tales of the Jedi characters Nomi Sunrider AKA Da Boda (name change due to copyright. Da Boda is ‘maiden name’), Arca Jeth, Knights of the Old Republic comics Vandar Tokar and more.
Hapan Gloves: Hapan is introduced as an insular cluster of planets in Courtship of Princess Leia. Items from Hapes would be luxury goods.
Rendili : Rendili watchman and other such vehicles first appeared in West End Game books and permeate the EU vehiclescape.
Carrick Station is named for the Knights of the Old Republic comic series Zayne Carrick.
Gav Daragon (ship) is named for the Hyperspace Explorer who (re) discovered the Sith in Tales of the Jedi, Golden Age of the Sith.
Balmorra: first appears in Dark Empire 2 comic books as a place with many corporations building war droids.
Carida (starship): The planet Carida is famous for being the Imperial Academy. It was destroyed in the Jedi Academy Trilogy. Famous graduates include Han Solo (Han Solo Trilogy), Kyle Katarn (Dark Forces Novellas/audio books). It’s not uncommon to name ships for planets.
New Cov Mission: New Cov first appears in Dark Force Rising of the Thrawn trilogy.
Killiks: first appear in Dark Nest Crisis set in the NJO era where there history is revealed. Joiners were a major part of the story arc.
Morgukai Nikto: first appear in the Republic Clone Wars comics. This branch of the Nikto is specifically a warrior who takes on Jedi. The Separatists were cloning them during the prequel era.
CorSec: short for Corellian Security, the name first appears in X-Wing: Rogue Squadron. Corran Horn was a member, as was his father and adopted grandfather. Corsec lasted until the rise of a New Republic when the Empire was phasing it out.
Corellian Jedi AKA The Green Jedi: the reputation of Corellian Jedi begins in X-Wing: Rogue Squadron. Their contrary nature is mentioned repeatedly in I,Jedi and Legacy of the Force: Betrayal. Nejaa Halcyon who appears with Anakin Skywalker in Jedi Trial was one of them. Here is a bit on the HoloNet news regarding them entering the Clone Wars: Archive
Flesh Raiders: appear again (or previously, depending on POV) in Dawn of the Jedi comics. They were introduced to Tython when the Rakata Empire invaded.
Trandoshans: while the species appears in the movies (Bossk) it is in the Bounty Hunter Wars and Tales of the Bounty Hunters novels that their culture of wookiee hunting and worship of the Scorekeeper evolve.
Chiss: Chiss first appear in the Thrawn trilogy novels. More of their cultural history appear in the Thrawn Duology, Survivor’s Quest, Outbound Flight and some in New Jedi Order novels. The first video game appearance ‘may’ be in the Dark Forces games as an occasional bartender.
Black Sun Crime Syndicate: was introduced as a multi species criminal Empire in Shadows of the Empire multimedia project. Xixor the falleen was head Vigo at the time but it also included notables like Durga the Hutt. It also gets attention in Coruscant Nights (another Hutt), a get out jail free card by the New Republic to help retake Coruscant in X-Wing: Wedge’s Gamble. It received a serious pruning of leadership and bodyguards (including a nightsister of Dathomir) by Darth Maul in the comics. It attempted to reform in the Young Jedi Knight books and was alive and active in the Legacy era, over 100 years after the New Republic and the original trilogy.
Names like Organa, Dodonna and Madine may be ancestors of those in the movies. Following on from that:
The House of Thul (Alderaan) : Raynar Thul is a Jedi in Luke’s New Jedi Order. He first appears as a student in Young Jedi Knights. He comes of a successful business family that runs the Bornaryn Trading Fleet.
Gormak Vandrayke: the Vandrake generator the Cedrax is trying to build comes from ‘Camper’ AKA Vandrayke, a genius gone into hiding in the Knights of the Old Republic comic series.
It may or may not be a coincidence.
Port Nowhere of the smuggler storyline has a very similar line to Fort Nowhere on Ruusan in the Dark Forces novellas and audio books. Both were founded by smugglers.