When the EDF soldiers are discussing their battle plan to kill the Cycloid Emperor, and forget what Phase 3 is. One trooper describes Phase 3 as "profit." This is a reference to a common internet meme in which numbered lists end with the second last entry being "???" and the final entry being "PROFIT!". This joke originates from an episode of South Park.
In the opening of the game, a few moments before you fight the first boss, the scene where the EDF and the Aliens are fighting is very similar to the "Halo: Combat Evolved" opening.
The videogame controller that Duke used after the introduction is similar to the Xbox 360 controller, with the buttons changed into the word of D.U.K.E.
In the beginning of the game, you can see TVs on the walls. The image on the screens is a reference to old-time television broadcast warnings. It is also a reference to Fallout 3.
In the elevators you can see a poster advertising "Hail to the King – The Musical", which is actually based on Duke Nukem 3D's boxart, which in turn is based on the poster for the movie Army of Darkness (note that this movie is also the original source of the quote: "Hail to the King, Baby!"). As a humorous side-note, Evil Dead and Evil Dead II (the movies that precede Army of Darkness), were also adapted into a musical.
The whining executive in the backstage of the "Damn, It's Late Show" is a reference to the Christian Bale tirade to a crew member during filming of Terminator Salvation.
Duke's encouragement to take "Vitamins" directed at the Duke Nukem fan kid is a reference to Duke Nukem 64 with the change of steroid pills into vitamin pills as the N64 console was seen as a "family friendly" console. This is also a reference from Hulk Hogan.
The computer asks for a red keycard, to which Duke replies, "Keycard? I don't need no fuckin' keycard!" This is a reference to the previous Duke titles that involved keycards to get through doors. It's also a clear allusion to a famous line from the 1948 movie adaptation of The Treasure of Sierra Madre, frequently misquoted as: "Badges? We don't need no stinking badges!" (the actual line is: "Badges? We ain't got no badges. We don't need no badges! I don't have to show you any stinkin' badges!" – the misquote, however, was further popularized by its use in the 1974 Mel Brooks movie Blazing Saddles).
The Hollywood Holocaust Stalker theme, among other iconic Duke Nukem 3D MIDIs are heard when playing Balls of Steel pinball, which is also the name of a 1997 Apogee-published pinball computer game.
Sometimes after killing a Pig Cop, Duke will utter "Porkchop Sandwiches!" He also will say "Body Massage!" after grabbing a vibrator in Duke's Titty City. Both are quotes from Fenslerfilm's G.I. Joe PSA parodies.
The door to the turret used during the Mothership Battle has a label above it, reading "Phased Plasma Cannon", "1.21 Gigawatts;" the second part clearly being a reference to Back to the Future.
After clearing the "Phased Plasma Cannon" chamber, Duke enters a numeric code to either unlock or start powering up the cannon. This code appears to be "1138," a number frequently found in works by George Lucas, taken from the title of his first film, THX 1138.
The "Phased Plasma Cannon" is probably a reference to the first Terminator film, where the Terminator asks for a "Phased Plasma Rifle in the 40 watt range."
When finding the Dead Space helmet, Duke will comment, "That's one dead space marine." This is also a reference to a similar comment he made in DN3D when finding a dead marine in Doom gear: "That's one DOOMED space marine."
The entire Hive level is an 'Aliens' reference.
The sphincter doors which Duke tickles open and purple spheres used to open some of them are a reference to Prey.
During the very controversal scene one of the octababies that emerges from the Holsom twin on the left immediately after her violent death is wearing sunglasses. The player really has to be paying attention to notice this.
This level with it's sphinter doors and pulsating sacs reminds some players of the Halo 3 level "Cortana". Same sort of organic design and atmostphere.
After the battle against the Alien Queen, while passing out, you can hear an allied soldier shouting his name ("Duke! DUUUUUKE!"). This could be a reference to the Game Over screen of Metal Gear Solid.
When coming face-to-face with the Alien Queen, Duke will say, "Baby, you make me wish I had three guns". This is a reference to Total Recall. It can also be seen as an ingame joke about Duke only being able to carry two guns at a time.
On the table next to the security camera viewscreen, the spinning top from "Inception" is permanently spinning around, indicating that Duke is dreaming.
In the level's intro, the stripper mentions that if Duke follows orders, there will be a lap dance... and cake; the latter being a reference to Portal.
In the level "Duke Nukem's Titty City" a man is found wearing a t-shirt, with a printed wrench on it. This picture is directly taken from the wrench kills achievement from Prey, another of 3D realms' games.
In the "Champagne Room," the player can explore the closed rooms. In one of the rooms, there looks to have been a crazy party. On the chair is a wrench from the Hangover when Stu pulls off his tooth.
If one of the cash dispensers is used twice, the sentence "Feed me a stray cat" will be shown. This is a reference to the movie "American Psycho".
Next to the spinning top there is an answering machine. If activated, it will say, "tonight......you," which is a reference to a Aqua Teen Hunger Force episode Handbanana where Handbanana's famous quote was "tonight......you."
In one of the restrooms is an exit door, over it is written "open dusk till dawn". This is a reference to the movie "From Dusk Till Dawn."
Near the glory hole there is writing on the wall "they live, we sleep." They Live is the movie where the quote "I'm here to kick ass and chew bubblegum, and I'm all out of bubblegum" came from.
The girl who says "Three days before I get married, I meet Duke" the guy who is standing next to her looks similar to Ray Stevenson - Punisher Warzone
On the restroom wall above a urinal, you can see written "JENNY 867-5309", a reference to Tommy Tutone from the 80's, as seen on the bathroom wall on Duke Nukem 3D.
There is a puzzle that involves turning a valve and Duke says “I hate valve puzzles”; this could be a reference to the Valve Corporation who have worked on the Half-Life series which also involves puzzles. Also Gearbox Software has worked with the Valve Corporation from time to time when developing games in the Half-Life franchise. The Valve Corporation also made Portal, which also features tough puzzles
Following the area made up by gears, fans, and pistons, shrunken Duke says "Duke one, Gears nothin'"; this could be another reference to the Gears of War franchise.
At the end of the level Forkstop there is a pink heart shape on the floor next to a locked closet. This can be opened with a barrel with the same mark and unlocks the achievement 'Companion Barrel'. An obvious reference to the Portal series.
When Duke climbs out of the water, entering a small room where you can see the giant monster wreak havoc, somebody can be heard screaming "My anus is bleeding!" which is a reference to a cartoon short by Don Hertzfeldt.
In the level Blowin' The Dam, the head from the psycho on the Borderlands cover can be found.
In Blowin' the Dam: Part 2 there is a reference to Donkey Kong and Mario where barrels are bouncing down a stair case and Duke quotes "Damn I wish I had a Hammer right about now", and when he gets to the top of the stair case he quotes "Oh, I was expecting a Monkey'.
One of Duke's many quotes when killing an alien is "I'm from Las Vegas, and I say kill 'em all!". This is a reference to Starship Troopers, where Johnny Rico says the same line but with "Buenos Aires" instead of "Las Vegas".
Another Lo Wang (and Highlander) reference when Duke perform an execution move, he will sometimes utter "There can be only one".
When the EDF soldier points Duke to Master Chief's power armor he will comment, "Power armor is for pussies".
One of Duke's lines is "If it bleeds, I can kill it." which is a reference to Predator.
"If I promised to kill you last, I lied" is taken from the Schwarzenegger movie Commando.
Another of Duke's many quotes when killing an alien is "Good, bad, I'm the guy with the gun.". This is a reference to a line from Bruce Campbell in Army of Darkness.
One of the "ogle" lines that Duke may say to his maid Kitty Pousoix is "Dear Diary: Jackpot!". This is a reference to Family Guy where the same line is said by Glenn Quagmire in season 3 episode "Peter Griffin: Husband, Father... Brother?" after finding a bound cheerleader in the bathroom stall.
The number 42 appears in several places in the game. This could possibly be a reference to Hitchhikers Guide to the Galaxy.
Jersey number 42 in the Detonators' locker room in Duke Lives is Allen H. Blum III, lead level designer of Duke Nukem Forever and the only person to have worked on the game throughout its entire production cycle of 1997-2011.
When picking up a power-up from an EDF crate, Duke sometimes utters "I'd buy this for a dollar," a reference to RoboCop.
After drinking a beer, Duke can sometimes be heard uttering "You're my boy, Blue!", which references a memorable line from Frank "the Tank", in Old School.
When you fight the Octaking and beat him the first time, Duke might say, "I'm not finished with you, Octapussy". Possibly a reference to the James Bond movie "Octopussy".
The Holsom twins are a reference to Mary-Kate and Ashley Olsen.
The Lo Wang Chinese takeout boxes that are strewn across the game is a reference to 3D Realms' Shadow Warrior protagonist.
In the My Digs section of multiplayer, the second unlockable babe - Miso Ho'ney - will say, "Who wants some Wang? Not me! I want some Duke!". This is another reference to Lo Wang from Shadow Warrior.
Another Shadow Warrior reference comes in the form of an trophy/achievement: Placing a trip mine on a live enemy will unlock the trophy/achievement named "Sticky Bomb like you"; the same phrase is said by Shadow Warriors' Lo Wang when placing a sticky bomb on a live enemy in his game.
The control layouts' names on the Xbox 360 version are references to other popular FPS games. For example, MC stands for Master Chief, and its button layout replicates Halo 3's default control scheme. The other layouts are Freeman, which replicates Half-Life 2's controls; and Duty Calls, which replicates Call of Duty's.
The cutscene after the final battle with the True Cycloid Emperor is a parody of Call of Duty 4 : Modern Warfare loading cutscene for the level "Aftermath" (in which Duke quickly breaking the fourth wall and snap at the player)
The number 69 is referenced many times in the game, most noticeably in the ammo count of the Devastator.