In Scarlet's Booty DLC there two are enemies called Mr.Bubbles and Lil' Sis, which are spoofs of Bioshock's Big Daddys and Little Sisters. When you defeat Mr.Bubbles without harming Lil' Sis you get a special reward.

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 reversal, 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", another reference to the Nintendo series Mario.

In the Caustic Caverns is a small island surrounded by corrosive waters. On the island is a bonfire, and a man sitting on the edge of a small cliff. Speaking to him does nothing, though you can find what looks to be a phantom resting the bonfire, a reference to the Dark Soul series.

In the Caustic Caverns, you can find 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. Killing them will give you a few items of loot, including a new head skin with a pixelated look.

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.

There is an easter egg in the Highlands when passing through the Hyperion base to the east. Looking over a cliff, you can see a small tent. Entering the tent triggers a double rainbow to appear on the horizon behind you, with a sound clip from either Handsome Jack or Claptrap imitating the Double Rainbow Youtube video.

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" after the rat master "Splinter", their surfer like language ("dude", "brah") and their craving for pizza used to lure them out.

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.

In Borderlands 2, There's a character named Michael Mamaril that will give you 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.

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.