An alchemist on Sentinel Island is named "Allan", who was the pupil of the alchemist "Walker". The main character of D. Gray Man is named "Allan Walker".
The quest "The Old Ghost and the Sea" is a reference to The Old Man and the Sea a story written by Ernest Hemingway. It features a ghost called Jonah(as in prophet Jonah) who got swallowed by a whale called Mocha Dick (as in the Moby Dick by Herman Melville)
Talking to one of the gossips in the Broken Valley Village will yield a dialog option that includes the word 'cake'. The gossip will respond by musing that 'the cake is a lie'; a clear reference to Valve's Portal.
The person in the Hall of Echoes is named Charon, Ferryman of the Acheron river in Greek mythology.
The Quest Saving the Bacon involves a pig named "Kevin". This is a possible reference to the famous American actor Kevin Bacon.
On Sentinel Island, the chef is Henry, his wife is Eleanor and she refers to their son Richard who "has quite the Lion's heart". Eleanor of Aquitaine married King Henry II of England and one of their sons was Richard the Lionheart.
When introducing himself, The Librarian in Maxos' Temple stumbles over the word "librarian", saying "Larian" by mistake, an obvious reference to "Larian Studios".
In the Tavern in Broken Valley Village, there is a knight who is a great hunter, who goes by the name Brave Sir Robin, and obvious reference to Monty Python's The Holy Grail. It is ironic however that unlike the character he was named after, this Brave Sir Robin is actually brave.
Outside of the Miller's house in Broken Valley Village there stand two woman, by a clothes line name Peggy and Sue, this is most likely a reference to the Buddy Holly song Peggy Sue.
In the tavern in Broken Valley Village, after completing the Band of Brutes quest there is a man by the name of Gondolf, who occasionally glows white, this is preceded by a large beam surrounding him. It is unclear if he is the one cause this, however by the fact that he is surrounded by magic one can assume that was named after Gandalf the wizard who accompanies the fellowship in the Lord of the Rings.
Once you have killed a fixed amount of rabbits, you will be attacked by Killer Bunny, who hits like a truck. Obvious reference to Monty Python's The Holy Grail.
Near Penelope's grave in Broken Valley you can meet a White Rabbit. If you follow him, he will lead you to a chest. It is a reference to Alice's Adventures in Wonderland by Lewis Caroll.
In the Tavern in Broken Valley Village, there are two men called Ollie and Stan. When mindreading Ollie, he "thinks" Hardy, and mindreading Stan reveals Laurel. Laurel and Hardy were two famous comedians/actors.
Turgoyn a maritime historian is a member of The Prancing Seahorse.This may be a reference to the name of a tavern in Bree, in Lord of the Rings: The Prancing Pony.
In Broken Valley map, you can see tag saying "To boldly go where no Rhode has gone before" an obvious reference to Star Trek's "To boldly go where no man has gone before"
In the Black Boar tavern, you meet two men named "Josh" and "Toby"...two of the main characters of the American TV series "The West Wing"
In Bandit Camp, where people are training to shoot arrows, two women are named "Thelma" and "Louise", an obvious reference to movie "Thelma & Louise".
In your Battle Tower, in Necromancer area, there is a man called Grimm. If you mindread him, he thinks "I hope my brother and me will be reunited one. Such stories I could tell.". Clear reference to Brothers Grimm.
The Dragon Terror Patrol fight is an homage to super sentai transformation and role-call sequences commonly seen in tokusatsu such as Kamen Rider and Power Rangers. This is also one of the few human fights where the player can finish off the enemy in dragon form--essentially having the dragon knight take on the role of kaiju. (Another staple of super sentai.)
The Flames of Vengeance expansion campaign starts off with the dragon knight teleporting into the game in a sequence that's identical to the teleportation sequence in The Terminator. The music that plays here is also a direct parody of The Terminator theme.