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.
Lore: the vast majority of the codex involves Tales of the Jedi and Knights of the Old Republic.
The Jedi Code first appeared in the Star Wars Role Playing game but the first novel use of it was probably Jedi Academy: Dark Apprentice. It afterward became the foundation of the Jedi Order, mentioned in many stories.
The Sith Code first appeared in Knights of the Old Republic. This continued use on to Darth Bane trilogy and into Legacy of the Force.
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, Master Chamma, Knights of the Old Republic comics and game Vandar Tokar and more.
Armor based on Expanded Universe characters:
Jori Daragon – Hyperspace Explorer, Source: Tales of the Jedi, Golden Age of the Sith
Gav Daragon – Hyperspace Explorer, Source: Tales of the Jedi, Golden Age of the Sith
Naga Sadow – Source: Tales of the Jedi, Golden Age of the Sith, Tales of the Jedi: Dark Lords of the Sith
Uliq Qel Droma – fallen Jedi/Sith/Redeemed Jedi, Source: Dark Empire, Tales of the Jedi: Knights of the Old Republic, Dark Lords of the Sith, The Sith War, Redemption, Clone Wars (game 2003)
Exar Kun – fallen Jedi/Sith/Sith Spirit, Source: Source: Jedi Academy trilogy (books), Tales of the Jedi: Knights of the Old Republic, Dark Lords of the Sith, The Sith War,
Mandalore the Indomitable – Mandalorean war chief , Source: Tales of the Jedi:Dark Lords of the Sith, The Sith War
Mandalore the Ultimate – Mandalorean war chief , Source: Knights of the Old Republic (comics)
Cassus Fett – Mandalorean, Source: Knights of the Old Republic (comics)
Zayne Carrik – Jedi padawan/henchman, Source: Knights of the Old Republic (comics)
Lucien Draay – Jedi Master of the Covenant, Source: Knights of the Old Republic (comics)
Jarael – Arkanian fringer, Source: Knights of the Old Republic (comics)
Ajunta Pall – Exiled Fallen Jedi/Founder of the Sith/conqueror of the sith species, Source: Tales of the Jedi, Golden Age of the Sith, Knights of the Old Republic (game)
Zoxann – Exiled Fallen Jedi/Founder of the Sith/conqueror of the sith species, Source: Tales of the Jedi, Golden Age of the Sith, Knights of the Old Republic (game)
Revan – Jedi/Sith/redeemed jedi/war hero and war criminal, Source: Knights of the Old Republic (game)
Jolee Bindo – former jedi padawan, self proclaimed exile and survivor of the Sith War, Source: Knights of the Old Republic (game)
Juhani – cathar jedi, Source: Knights of the Old Republic (game)
Mission Vao – Twilek fringer, Source: Knights of the Old Republic (game)
Bastila – Jedi Knight, Source: Knights of the Old Republic (game)
Calo Nord – bounty hunter, Source: Knights of the Old Republic (game)
Carth Onasi – pilot/soldier, Mandalorean war, Source: Knights of the Old Republic (game), Knights of the Old Republic 2 (game)
Nihilus – Sith, Source: Knights of the Old Republic 2 (game)
Atton Rand – fringer, Source: Knights of the Old Republic 2 (game)
Atris – Jedi Master, Source: Knights of the Old Republic 2 (game)
Visas Marr – Jedi, Source: Knights of the Old Republic 2 (game)
Kreia – jedi/sith/mystery Source: Knights of the Old Republic 2 (game)
Karness Muur – sith lord, Source: Knights of the Old Republic (comics) (Vector cross over with Dark Times, Rebellion, Legacy series)
Tund Sorceror – mysterious race with ties to the Sith, source: Lando Calrissian and the Mindharp of Sharu.
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.
Model Starships (pet): The Ebon Hawk – Source: Knights of the Old Republic 1 and 2.
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.
Korriban: first appears in Tales of the Jedi: Dark Lords of the Sith and Dark Empire 2. Its also explored in Golden Age of the Sith, Knights of the Old Republic 1 & 2, Jedi Academy (the game), visited in Jedi Quest series by Jude Watson and many other places. Sith Warrior and Sith Inquisitor both begin on this world in this game.
Taris: first appears in Knights of the Old Republic. What you see in SWTOR is how it was left due to events in KOTOR. There is class story and planetary story here. One of the minor story arcs you can play in that game has a corresponding minor quest on this you can follow to find out what became of people you met if you played the other game. (warning. It’s depressing.)
Ilum: first appears in Jedi Quest: The Path to Truth and Genndy Tartoski’s Clone Wars Microseries as a kind of sacred place Jedi to gather lightsaber crystals and see visions. In game it continues to do so, with the Empire and Republic warring over the crystals.
Nar Shaddaa: first appears in Dark Empire as the world Han and Chewie hung out on when beginning their smuggling career in earnest. It’s further fleshed out in the Han Solo Trilogy by Ann Crispin.
Hutta AKA Nal Hutta: first appears in Dark Empire, also mentioned in Han Solo Trilogy by Ann Crispin and Dark Saber.
Ziost: was first established in Tales of the Jedi Golden Age of the Sith as one of their worlds.
Kuat Shipyards which has its own flashpoint first appears in the Bounty Hunter Wars Trilogy.
New Cov Mission: New Cov first appears in Dark Force Rising of the Thrawn trilogy.
Killiks: first appear in Dark Nest trilogy 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 with bad grammar.
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 (title) 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.
Selonians and Drall first appear in The Corellian Trilogy of books, the first time the world and cultures were ever fleshed out. Human Jedi, Rogue Squadron Pilot and Corsec member Corran Horn even dated a selonian which is mentioned in I,Jedi.
Genoharadan is a secret bounty hunter guild with an interest in influencing Galactic Politics via assassination. you can first meet during Knights of the Old Republic
Rakata: first appear in Knights of the Old Republic (game) and get greatly expanded on in game, especially during quests such as Tatooine, Nar Shaddaa and the Forged Alliances Flashpoint.
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.
Revan goes back to the main character Knights of the Old Republic. The Force Ghost of the Exile (AKA Meetra Surik) goes back to Knights of the Old Republic 2. Both they and Lord Scourge are the focus of the novel Revan.
Exar Kun, Marka Ragnos, Naga Sadow all are Sith spirits floating about Yavin 4. These characters came from Golden Age of the Sith and Tales of the Jedi. Ragnos would be seen again as a spirit in Jedi Academy (the game) as would Exar Kun, in Jedi Academy (the books)
Theron Shan got his start in Dark Horse Comics, The Lost Suns, followed by SWTOR Annihilation (novel) before appearing in the game as a recurring character and finally as a companion.
Bao Dur gets a mention as Ogoruub the Hutt recieved the Bao Dur Science Prize. Bao Dur was a companion of the Exile in KOTOR 2 who served as an engineer in the Mandalorean War.
Boma beast first appears in Tales of the Jedi: Knights of the Old Republic.
Rancors appear in Return of the Jedi, but the first idea to ride them comes from The Courtship of Princess Leia. The witches of Dathomir used them as mounts.
Kybuck first appeared as Yoda’s mount, given him by the wookiees, in the Genndy Tartroski Clone Wars Microseries.
Thranta: first mentioned in McQuarrie paintings but also in The Illustrated Star Wars Galaxy and seen off Alderaan in the Young Jedi Knights series.
Terentatek first appear in Knights of the Old Republic.
Tukata first appear in Tales of the Jedi guarding Korriban’s tombs.
Kath hounds first appear on Dantooine in Knights of the Old Republic.
Rakghouls first appear in Knights of the Old Republic. They also feature in the comics in a cross over event between several eras of the saga, beginning in KOTOR comics and ending in the Legacy era.
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.