During this mission, you'll encounter Benny the Booster. This may or may not be a reference to Boosters, a type of video game cheater who plays dishonestly or with friends in an effort to boost their stats or level. It is also a common term for people who get together to unlock achievements in multiplayer games without playing a legitimate game.
After killing Benny the Booster, Captain Scarlett will make a reference to missing "Bowsers seven through 13" which were her puppies. Bowser is clearly a reference to Bowser of Mario fame. In this instance, it's a double joke because of the prevalence of the name "Bowser" as a dog's name.
Your second target is ol' Deckhand. There is no reference here but the name is a pun on the title "Deckhand" which is an old indescript title for the common and generally unnoticed pirates who work on the deck of a ship.