In the mission "Splinter Group" the four mutated raiders that you must kill are named "Mick, Lee, Ralph, and Dan" this is a play off of the Teenage Mutant Ninja Turtles named "Michelangelo, Leonardo, Raphael, and Donatello". The other similarities include: their hideout being in the sewers, their name "Splinter Group" , along with a hidden Easter Egg found later in their lair of an enemy named "Flinter", after the rat master "Splinter", their surfer like language ("dude", "brah") and their craving for pizza used to lure them out.
There is a reference to the movie, Seven. On a platform/balcony, you will see a box, if you open it, there will be a skull with hair on it. Upon opening it, Handsome Jack will exclaim "Awwwww! What's in the box!?!?"
The villain, Handsome Jack was initially inspired by an interview of actor Nathan Fillion on Jimmy Kimmel Live! He was described as acting "charming and funny, but also slightly arrogant in a down-to-Earth kind of way". He was originally conceived to be a vault hunter who would pop in and out of the story to both help and hinder the heroes but his role was revised as the game developed and is voiced by actor Dameon Clark. He is often listed as one of the greatest video game villains.
An NPC named Michael Mamaril can be met in Sanctuary. He is named after a late fan of the first game also named Michael Mamaril. Michael passed away of cancer at the age of 22 in October 2011. Gearbox also posted a eulogy for him online voiced by his favorite character, Claptrap.
In Moxxis bar, in Sanctuary, a pizza box can be found on one of the tables.
Scanning the QR code present on the box gives the following quote:
Wise man say, forgiveness is divine but never pay full price for late pizza. -Captain Picard