Borderlands/Shout Out

The entire game is crammed with them, to the point that it's easier to list which parts of the game aren't Shout Outs. Also, we have nowhere near all of the shout outs, so this page will take a very long time to be finished. A ~~few~~ bunch of examples, sorted by reference subject:

Anime and Manga

If a player gets more than 9000 kills online, his profile will read "Kills Over 9000".
"This is not a planet of peace and love."
- One of the challenges for inflicting damage is "Human Tsunami". In the series, the main character is believed to be so destructive, he's classified as "The Humanoid Typhoon", making him the first human being to be registered as a natural disaster.
The black Runner color-scheme names it "Vehicle X".

Television

Baron Flynt's two musclebound bodyguards are named Hanz and Franz.
The achievement Truly Outrageous.
Rebel Claptraps in DLC 4 yell "Hey baby, wanna kill all humans?" and "Exterminate!"
One mission has you kill Jaynis Kobb. You even find him in Jaynistown.
The Misery Machine and anything related to it in The Zombie Island of Dr. Ned. An ECHO had one of the former occupants exclaiming Shaggy's trademark "Zoinks!" - and he has a pet skag named Skaggy.
In the hospital part of DLC 1, the hospital's name is Generally Hospital. And appearance-wise, the hospital is creepy and kooky, mysterious and spooky.
The first thing Patricia Tannis says as she walks in during her cutscene is "Atomic batteries to power, turbines to speed!" from the 60's Batman TV show / movie.
Whitting's Elephant Gun: "Why don't you go shoot yourself an elephant?"
The achievement entitled Can't We Get Beyond Thunderdome?
The orange color palette for the Runners is called "General Flee", complete with a "01" on the side.
Sledge will occasionally shout "The burning lets you know its working!", a reference to a well-known Head and Shoulders commercial slogan.
The end of DLC 3 concludes with a time-based scavenger hunt through Knoxx's secret armory, run by Marcus Kincaid. The name of the game? "Super-Marcus Sweep"

Film

Patricia Tannis says "We'll need a nuclear reactor to generate the One point twenty-one jiggawatts -- Oh, hey!"
When you talk to Mr. Blake in the Claptrap Rebellion DLC, he says that without phase 1 complete, there can be no phase two or three, and phase 4 is right out.
The hidden basement has a leg lamp, a Christmas tree, and a bee bee gun like in A Christmas Story.
- The Rider: You might put someone's eye out.
One of the mission descriptions includes the phrase "a wretched hive of scum and villainy."
- A random Bandit also once shouted "Blast him!"
- The Lancer vehicle's White/Beige color-palette is called "Stormtrooper".
Baron Flynt's Shotgun is called a Boomstick
- And the description is, of course, "Beyond Groovy"
One of the quotes upon being revived is, "Only a flesh wound."
The Dove. "Sometimes, I forget to reload."
The Torgue Violator ("Your move, creep.") as well as the Torgue Cobra ("I LIKE IT!", a reference to the Cobra Assault Cannon from the movie and the thug who was more than happy to test it out.)
The S&S Gemini ("Double Whammy")
There's someone in the game called Bruce McClane.
- During the quest he appears in, the Player Character has to collect poisoned cigarettes because "some kid could find them".
The game even has pure visual shoutouts - the Crimson Lance comes with posters that reference District 9. Considering D9 came out only a few months before the game did, Gearbox was essentially adding in new art assets and shoutouts right up to the last possible moment.
The Ludicrous Speedway
- Also the Achievement/Trophy "Hot! Too Hot!"
- The challenge of shooting 25,000 times is titled "Who made that man a gunner?"
- and its next-highest challenge award: "Keep firing!"
All of Brick's tier 4 skills are movie references: Blood Sport, Unbreakable, and Master Blaster.
- Salvador follows suit in the sequel, with many skills that are movie references. Among the ones revealed in the E3 gameplay demonstration are Yippee-Ki-Yay, Out of Bubblegum, andJust Got Real
Every now and then, bandits will shout at the player "I'll take pleasure in gutting you, boy!"
Chuck Durden, the fighting ring owner.
The Jakobs Unforgiven revolver and its description "It's a helluva thing..."
Three boats you have to destroy at one point: the "Righteous Man," the "Great Vengeance" and the "Furious Anger."
- Not to mention the trophy/achievement for completing the first DLC: Ned's undead, baby, Ned's undead.
Mad Mel.
- Before facing him, the player is forewarned that he is a "Lethal Weapon" in any vehicle, and after his defeat Helena is thankful that somebody "with a Braveheart" stood up to him.
- The fact that he's a vehicular combat expert is probably at least a little in reference to Mel Gibson's infamous drunk driving incident. Or maybe he's just a Road Warrior.
The Pestilent Crux Shotgun has the caption Bring out your Dead!
The Eridian Lightning has the caption "I feel like I'm gonna break this damn thing"
The Chiquito Amigo's 'Say "Hello"' caption seems innocuous enough, until you take into accound that Chiquito Amigo translates as 'Little Friend' to which you realise its a subtle reference to Tony Montana's infamous line "Say Hello To My Little Friend!"
The quote for the Hyperion Invader "BAM BAM BAM BAM BAM!" resembles a scene in the movie Reservoir Dogs where hired gun Mr. White, furious at Mr. Blonde's earlier shooting of several hostages, re-enacts the scenario by using his hand as a gun and shouting "BAM! BAM! BAM! BAM!"
"I have you in my eye, Sir" for the Atlas Cyclops sniper rifle is from a line by Dr. Willis warning George III to do as he's told in the the 1994 film The Madness of King George.
The Bandit-traps sometimes shout "Come with me if you want to die!"
Another randomly-spouted Claptrap line is "Oil can! Oil can!"
- Ironically enough, one of the items Rebel Claptraps will randomly drop is, you guessed it, an oil can.
Steele-Trap says "Kneel before Steele" while fighting her.
A (falsely) injured rebel Claptrap you can save sings "Daisy, Daisy, give me your answer do..."
Skagzilla and Mothrakk.
The achievement/trophy entitled "There Are Some That Call Me... Tim."
Another achievement is called Pandora-Dog Millionaire.
Zombie T.K. Baha talks about all the ways one can cook and serve brains.
Crazy Earl mentions that Krom "...made me an offer I couldn't refuse."
During Mad Moxxi's Underdome Riot, she'll occasionally remark "You- you've earned it..." when she drops party-favors for you.
- Also during the Underdome Riot, Round 18 is titled "Game over, man. Game over."
Repair Kits: It's Got What Claptraps Crave!
Another achievement is titled "You call this archaeology?"
The Torgue Friendly Fire shotgun has the flavor text "Have a nice day." It also fires smiley-face shot patterns.
Crimson Lance officer Master McCloud is known to have said "Death is the only way out..."
Mission from the Zombie Island of Dr. Ned: "Night of the Living Ned".
Moxxi: "Who loves you and who do you love?"
One of the challenges for buying and selling items is titled "How Much For The Gun?"

Literature

Baha spelled backwards is 'Ahab', and T.K. has a fascination with killing a monstrous creature that ate his leg.
"Now it's time for my pound of flesh!"
T.K. Baha's late wife's gun, the 'Lady Finger', has "omnia vincint amor"
In the Purple Juice! mission, the four pumps that must be restored are named Brandybuck Pump, Took Pump, Gamgee Pump, and Underhill Pump.
- You also fight a unique Spiderant boss named "Helob".
- In the Zombie Island of Dr. Ned DLC, one of the things Zombie TK can say about brains when you enter his house is "Boil 'em, mash 'em, stick 'em in a stew."
- The Secret Army of General Knoxx DLC takes you to the Pipp Inn.
There are a large amount of Shoutout to Hitch Hikers Guide to The Galaxy. One of the Claptraps you can rescue repeats nearly word-for-word Marvin's speech when he first meets Arthur Dent. And I've seen a couple of signs that say "Don't Panic", in large friendly letters to boot.
- Tannis needs you to help her fix her infinite improbability device in Claptrap's New Robot Revolution.
Challenge award and achievement "How much for the planet?" references a humorous Star Trek tie-in novel called "How Much For Just The Planet?" by the late John Ford.
Written on the walls of some of the early houses are the words "turtles all the way down".
Whitting's Elephant Gun could be based on Ernest Hemingway's "Hills like White Elephants". Evidence of this includes: 1. The gun's name is "Whitting's Elephant Gun", which could reference "Hills like White Elephants" 2. Ernest Hemingway was a noted "Big Game Hunter", which is also the title of the mission where you have to kill Skagzilla, which leads to you acquiring the gun as a reward and 3. The mission is given by a man named Ernest Whitting.
The mission in DLC 4: "Spa vs. Spa."
In DLC 3, you are assigned a mission to destroy 5 public surveillance cameras. The mission name? "Big Crimson Brother is Watching!"

Music

The Dahl Anaconda is "long and strong."
The mission "Fight For Your Right to Part-E" from DLC 4.
The trophy "You're On A Boat!" exists purely for this shoutout.
The Eridian Flaregun from the 3rd DLC has "Smoke on the Water...", making it a double-reference:

Lyrics: "...some stupid with a flare gun burned the place to the ground..."

The flavor text on the Dahl Penetrator reads "Sniper Killer... Qu'est que c'est."
Early in the game you're assigned the mission "Schemin' That Sabotage"
Upon leveling up, Roland occasionally remarks "Gettin' better all the time!"
The Maliwan Hellfire SMG has the flavor text: "We don't need no water...", referencing The Roof Is On Fire by Rock Master Scott and The Dynamic Three.
Sledge comes back wrong in DLC 4 to serve the Robo-lution as Motorhead. He also occasionally drops the ridiculously fast-firing machine gun, 'The Chopper'.

Video Games

DLC 3 has 'Road's End', with highway signs like "Road to Hill 30" and "Hell's Highway"
The Hyperion Butcher, with special effect text "Ahh... fresh meat!"
- Also Rakkinishu, which has a guaranteed drop: the unique "Cracked Sash" shield mod.
- One of the Lancer's paint-schemes is called 'Diablo', and yes, it's red.
Dr. Ned: "Oh come on! Don't act like you've never had to wait for a hand-cranked elevator before!"
The game opens with the Guardian Angel saying "Would you kindly fix that poor robot?".
- The audio recorders look a lot like the ones you would find in Rapture, as well.
- This quest could very well be a reference to the shops found throughout Rapture.
- Atlas is in control, and it initially seems to be helping you (well, the guns, anyway), but later it's trying to kill you.
- "Is a Claptrap not entitled to the oil of his brow?..."
The Circle Of Duty missions in DLC 3; the last mission is even called "Circle of Duty: Medal of Duty"
Dumpster Diving For Great Justice.
- "Athena Set Up Us The Bomb."
House of the Ned in DLC 1.
The Torgue Twisted ~~Redeemer~~ Redemption has the caption "Monster Kill!"
Rhino rocket launcher could have not been a Shout-Out... in any other game, that is.
One of the control schemes you can select is called Angelic.
- Another one is named Resistant.
- And the third is Nuked.
"Earl needs food...Badly"
When you score a critical hit on a rebel Claptrap, they'll exclaim: "Whoa, System Shock!"
The overall look of the Crimson Lance is awfully familiar to the HelghastEmpire Army
Roland, on finding a health vial, will occasionally shout "Alright! HEALZ!"
The Hyperion Nemesis repeater pistol bears the description "There is no escape" -- in reference to Nemesis from Resident Evil 3: Nemesis
The achievement named My Brother is an Italian Plumber -- kill an enemy by stomping on its head.
The red Runner color-scheme names it "Blaster Master".
- The blue scheme for the Racer names it "Blue Blur".
- The brown color-palette for the Runners is called "Range Racer".
The challenge award for gets 250 kills with Incendiary weapons is named "Toasty!"

Tabletop RPG

The Powered Armour suits used by the crimson lance in the latest DLC look an awful lot like Adeptus Astartes power armour, also the suits care called 'devastators' which happen to be names of the Adeptus space marines who carried the biggest guns.
- Once the Crimson Lance start spawning in the Salt Flats, they are surrounded by what look like very thinly disguised Space Marine drop pods.

Memes / Internet Culture

The Final Boss of the Robo Revolution DLC may sometimes say "Looks like you're writing a suicide note. Would you like some help?" as a shout out to the infamous Microsoft Word mascot helper, Clippy.
One of the zombies in the first DLC looks awfully similar to a certain kid who likes turtles.
Explosives Challenge: "Boom Goes The Dynamite"
A potential self-referential Shout-Out: During Mad Moxxi's Underdome Riot, if you kill a Bandit with a headshot using Revolvers, the crowd will cheer "Heyooo!" in response.
Mad Moxxi's first husband is described as a cheat. In the cutscene, he is killed with the Konami Code.

Tarot

Tarot cards get a shout out when you find T.K. Baha's body in a position almost exactly like The Hanging Man.

Real Life

The Atlas Patton. ("May God have mercy on my enemies, because I won't" was supposedly said once by General George S. Patton, hence the name. The Other Wiki claims it was also once uttered by Queen Elizabeth the First.)
- Double reference in that the Patton always spawns as a revolver with a nickel-plated body and an ivory grip, referencing the two revolvers (in the same style) which Patton himself owned.
The two "Claptrap, Behind the Scenes" miniclips are Shout Outs to the infamous Christian Bale rant.
- The second one also contains a shout out to the infamous Bill O'Reilly rant, "We're doing it live!"
When one of the rebel Claptraps die, they might say "I see three... flashing red lights..." Now what does that sound like to you?
Whitting's Elephant Gun: an Elephant Gun is actually a real life type of rifle for hunting big game (e.g. elephants), Skagzilla could easily be classified as such.
The green Runner palette, "Mean Green", has a strong resemblance to a P40 Warhawk.
In DLC 3, at "Road's End", the player will spot a highway sign reading "Fort Knoxx - 20km". Fort Knox is an actual United States Military post, known for its proximity to the United States Bullion Depository. General Knoxx's unique, highly-valuable pistol ("Knoxx's Gold") is a further reference to this location.
There is a location on Pandora known as "Treacher's Landing", which is a possible reference to Arthur Treacher's chain of seafood restaurants.
You fight a massive Scithid on the "Trashy Knoll."
Marcus wants you to gather up Skag musk-glands and Rakk-hive ambergris to brew up a "...truly potent cologne." The mission name? "Old Spicy".
One of the challenges for scoring kills is titled "Your Kung-Fu is Best". This is a reference to Kevin Mitnick, a computer security consultant and author. He was previously a well-known computer hacker and 'phreaker', and prior to his arrest, he left a message on the investigating detective's answering machine, stating "My kung-fu is best!"
- Another challenge (this one for dealing Shock damage) is titled "Nikola Tesla is a friend of mine."
- Yet another (for sheer number of enemies killed) is titled "Now I am become Death...", a phrase uttered by J. Robert Oppenheimer.
One of Brick's skills is called "Sting Like A Bee."