According to "Inside the Vault: The Art & Design of Borderlands 2" that comes with the special edition of Borderlands 2, when the boss "BNK-3R" makes a noise, it's actually the game's sound designer Joshua Davidson yelling about tea.

In Borderlands 2, There's a character named Michael Mamaril that will give the player free (and usually rare) loot. This character is based on a real-life person who died at the age of 22. His friend wrote to Gearbox, the game's developers, asking them to do a eulogy using the voice of the fan-favorite character "Claptrap". Gearbox not only fulfilled his request, but also added Michael as a character in Borderlands 2, so he could live on forever in Borderlands.

There are a number of QR codes scattered around Pandora. Scanning these codes using a QR code scanner will result in different messages.

Pizza Boxes: "Wise man say, forgiveness is divine but never pay full price for late pizza. -Captain Picard."
Possibly a reference to 4chan, where many pictures of famous characters are misquoted. In this case, a Michelangelo quote from Teenage Mutant Ninja Turtles and Captain Picard from Star Trek: The Next Generation.

In Zed's Pharmacy: "Thank you so much for playing our game, now I'm rich with love AND money! !!Nick Wilson!! Ditto!!!"
A reference to the artist Nicholas W., an artist at Gearbox.

Various Places: "NICK WILSON/ /HO OH"
Same as the previous message, a reference to Nicholas Wilson.

The targets of the mission "Splinter Group" are four mutated raiders 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" after the rat master "Splinter", their surfer-like language ("dude", "brah") and their craving for pizza used to lure them out.

There is a small tent located in the Highlands. Entering the tent triggers a double rainbow to appear on the horizon, with a sound clip from either Handsome Jack or Claptrap imitating the Double Rainbow Youtube video.

In The Fridge, there is a quest related enemy named Laney White, accompanied by 7 midgets, each named with a foul adjective. This is likely a play off of Snow White and the 7 Dwarves, further implied by the related achievements, "Fairest of Them All", and "It's Off to Hell We Go".

In the Caustic Caverns is a cave with a number of pixelated blocks. These look very similar to blocks from Minecraft, which break when punched a number of times. Behind these blocks are a handful of enemies called Creepers, including a Badass Creeper, a kind of enemy also found in Minecraft. Among the loot they drop when killed is a new head skin with a pixelated look.

An enemy that can randomly spawn in the Eridium Blight map is called Donkey Mong, an obvious reference to the Nintendo character "Donkey Kong". Not only is his name just a simple letter replacement, but he attacks the player by throwing barrels, similar to Donkey Kong's first title. Upon killing Donkey Mong, the player will earn the achievement "Definitely An Italian Plumber", a reference to the Mario series, also by Nintendo, as well as an achievement in the first Borderlands, "My Brother is an Italian Plumber".

In the Scarlet's Booty DLC there are enemies called Mr.Bubbles and Lil' Sis, which are spoofs of Bioshock's Big Daddies and Little Sisters. Defeating Mr.Bubbles without harming Lil' Sis will give the player a special reward.

The Wildlife Exploitation Preserve may contain two enemies called Pimon & Tumbaa. This is a reference to the characters Timon & Pumbaa from Disney's The Lion King.

On the radio dials, each number goes up by a hundred until it reaches 800 where then it moves straight to 9001. This is a possible reference to the line "It's over 9000" from "Dragon Ball Z".

Psychos will sometimes say "Never gonna give you up" when they die, a reference to the song "Never Gonna Give You Up" by Rick Astley.

Occasionally, one of the citizens may say "I'm missing the new episode of Constable What!", a parody of the series "Doctor Who".

At the main menu, Claptrap can be seen entering an outhouse which will then suddenly vanish and quickly land back to the ground, a possible reference to the TARDIS from "Doctor Who" which also travels in a similar fashion.

In the side mission "Hell Hath No Fury", after blowing up the dam, Handsome Jack will read out a list of the week's construction casulaties which are: Hartnell, W. Troughton, P. Pertwee, J. Baker, T.

This is a reference to the actors William Hartnell, Patrick Troughton, Jon Pertwee and Tom Baker, all of who played in respective order the character 'the Doctor' in the science fiction series Doctor Who.

The challenge "Say Watt again" is reference to the film Pulp fiction where Jules Winnfield says it during an interrogation.

The side quest "3:10 to Kaboom" is a reference to the movie 3:10 To Yuma.

Upon using Zer0's deception skill he may say "How Hilarious. You set off my trap card. Your death approaches." This is a reference to the Yu-Gi-Oh anime.

There is an unlockable color scheme for Zer0 titled "Why So Serious?" This is a reference to the film The Dark Knight and the Batman franchise, as it is a line used by the Joker. The color scheme also uses similar colors to the Joker.

Upon exiting Dr. Zed's vending machine, it will sometimes state "Who needs a medical license when you've got style?" This is a reference to the internet meme "Who needs 'X' when you have Swag?"