The Matrix - Parody of that film appears in Escaping the Prison when Henry fights the prison chief.
Mulan - in Infiltrating the Airship, there's a medal called "Famous Movie Line" which involves failing to use a ninja star then spelling "Mulan" out of the words. This comes after Henry misses to kill a Toppat Clan member on a very short distance, after which the narrator says "How could you miss he was three feet in front of you", which is a line from that movie.
P.I.X.A.R. films - Number A113 is shown in FtC. The same number appears hidden in almost every P.I.X.A.R movie.
Predator - A Toppat member in FtC yells "Get to the airship!" the same way and accent that Arnold Schwarzenegger had in the first Predator when he yelled "Get to the chopper!"
Spider-Man - Henry attempts to throw web in FtC but fails because his hands are captured.
Spy Kids - When Henry uses Jet Boots, it is similar to the ones used in Spy Kids. In Escaping the Prison, Henry used a Jetpack, which is also similar.
Star Trek - After Henry betrays the government and flies off in enemy airship, Captain G yells Henry's name the same way Captain Kirk yells Khan's name in Star Trek II: The Wrath of Khan.
Star Wars- Ellie can use Force Choke Henry to lift him in to upper ground in Fleeing the Complex.
The Devil's Advocate - In Escaping the Prison, Henry has Kevin Lomax (main character from the movie)'s number as a lawyer contact in his cellphone.
The Good, the Bad, and The Ugly - Henry has a stand off with the prison chief, set to the movie's theme in Escaping the Prison. That scene also has similar showings of their faces, like in the iconic scene from the movie.
The Lord of the Rings - Gandalf's name can be seen in the metal bend fail screen in Infiltrating the Airship. "You're a wizard, Harry" - Gandalf, is written in parody, although it's actually a Harry Potter quote.
Animaniacs - When Henry gets chased by police in EtP, it is similar to how Ralph chases the Warners.
Avatar: The Last Airbender - Metal benders in the show have the same power as Henry. Earthbending appears as an option in Fleeing the Complex.
CSI - In the Center for Chaos Containment, the boss puts on sunglasses just like Horatio Caine.
Dragonball Z- In Stealing the Diamond the boss from the Center for Chaos Continment says "It's over 9!" a parody of the quote "It's over 9000!".
Family Guy - In Infiltrating the Airship when Henry chose the Stretch'um Chewies, and got his hand stuck on the gears. The fail screen shows "This really grinds my gears." Which is what Peter Griffin said in Family Guy, which later became a meme.
Futurama - Hyper-Chicken, one of the lawyers from the series, is one of the attorneys from Henry's phone.
Inspector Gadget - A shrink ray is an option, similar to Dr. Dummkopf's shrink gun.
King of the Hill - Hank Hill is one of the characters from the series and one of his quotes and his name appears in the game after one of the fail scenes in ItA.
SpongeBob SquarePants - A Magic Pencil appears in the SpongeBob SquarePants episode "Frankendoodle", and is an option in Infiltrating the Airship and the laser cut option fail quote is a meme from the episode SpongeBob, Sandy and the Worm.
Ace Attorney - Character Phoenix Wright, who appears as an actual character in the game, and Henry's lawyer in the trial, is actually based on the character from that game series. Henry also has Apollo Justice (another character) in his cellphone. The whole trial scene, including the courtroom interior, intro and the Judge, is based on Ace Attorney.
Advance Wars - A battle scene similar to those from this game can be seen in FtC when a tank shoots Henry.
Angry Birds - In Fleeing The Complex, Henry uses a Slingshot to get to the airship.
Animal Crossing - A Gyroid can be seen in the airship vault.
Banjo-Kazooie - The Clawpack looks like Kazooie and the fail screen mistakes him for a bird.
Bomberman - A bomb just like bombs in Bomberman is seen in the grapple option in ItA.
Call of Duty - One of the fails in Stealing the Diamond involves a Tactical Nuke - a rather infamous killstreak in Call of Duty: Modern Warfare 2 that requires 25 kills, in most situations gained by lucky camping, hence the fail description. In Fleeing the Complex, if you choose the crossbow for Ellie and the sniper rifle for Henry, he spins multiple times in the air before taking the shot. This is a reference to trickshooting/quickscoping from said series of the shooter games, which involves sniping people in such a stylish fashion, often called "360 noscope".
Castle Crashers - The Sandwich which powers Henry in FtC is an item from the game.
Counter-Strike - in Infiltrating the Airship, flashbang is an option, and "Fire in the hole!" is an audio file directly extracted from the game. In FtC, International Rescue Operative, Charles will help Henry to snipe the guard in the way, in which it uses the AWP sound from CS:GO. But ends up shooting Henry instead.
Donkey Kong 64 - The Golden Banana appears in the Banana Bomb fail screen. Also, when you click on the "OOH,BANANA", a banana that has the Nintendo 64 logo on it.
Earthbound - When Henry fights with Toppat leader, the way he is fighting is actually based on Earthbound (also known as Mother) game.
Five Nights at Freddy's - In Fleeing the Complex, there is a scene in which Henry runs towards a building with Freddy Fazbear in it. Freddy's scary face will be popping up on the screen just like in the game, as long as the player doesn't move on.
Final Fantasy - When Henry battles the Right Hand Man in ItA and chooses the sword, the same interface and Sound effects as the Final Fantasy NES/SNES is shown. Also, in FtC, when using the Shadozer, it plays a short remix of Shadow's theme from the same game.
Fire Emblem - When Henry battles Karlov in FtC the same interface and music from Fire Emblem are the reference.
F-Zero - One of characters from that game, Captain Falcon, can perform moves Falcon Punch, Falcon Kick and Falcon Knee which also can be done by Henry in ItA, StD, and FtC.
Grand Theft Auto V - When police chases Henry in StD, you can find stars just like in GTA. And in Fleeing the Complex, Henry will be knocked out by a stone and the word "wasted" can be seen in the earthbend option, along with sound effects. All that is based on death scenes from GTA V.
Half-Life - In Stealing the Diamond, a crowbar appears that spawns headcrabs afterwards. In Infiltrating the Airship, using a smudged CD in one of the endings loads G.A.B.E.N. (which is nickname of Gabe Newell, founder of the Valve corporation that made Half-Life series) and then HL3 fails to load. Half-Life 3 is actually one of the most infamous vaporwares, hence the fail. A Gravity Gun is one of the choices in the Grapple path of Infiltrating the Airship. Moreover, many sounds (machine ambiance in Chaos Center in Stealing the Diamond, door closing sound when the Toppat Leader closes the doors, using the card to open the door after Bone Melt choice) come from Half-Life. Also, in Fleeing the Complex, man with a briefcase can be found in multiple scenes. This is refrence to G-man, a mysterious character from Half-Life. This was added because Half-Life takes place in a complex Black Mesa.
Halo - When the police chases Henry in StD, you have an option to choose the sticky grenade. The only grenades that are blue and have a blue explosion are from Halo and in FtC Bubble Shield appears from Halo 3.
Heartstone - Talk between Isaac and the other guard in FtC is about Heartstone gameplay although the name isn't mentioned.
Hitman - "Allan please add details" is a message seen in one of the fails in ItA. It's a reference to Hitman: Blood Money, where a developer working on the game wanted someone called Allan to add a description to an item, but he did not, and that line later remained in the completed product.
Kirby - In FtC, Presumed Dead, at the final part, a Warp Star is presented as an option, which is from Kirby.
Kerbal Space Program - The rocket in the docks and how Henry crashes it in attempt to blast off is a reference to this simulation game.
L.A Noire - When Henry and Ellie try to blend in as guards in Fleeing the Complex, one of the guards calls out their disguise while "Doubt" pops up in the upper left on the screen complete with sound effects, just like in L.A. Noire.
LEGO Racers - There is a warp option in ItA that is the same as the game. It also shows a LEGO brick in the option screen.
Left 4 Dead 2 - In FtC, Convict Allies, the part where Henry has to rescue Ellie from a warden. The adrenaline, which appears in Left 4 Dead 2, is presented as an option. Also, the part where Ellie smacks a warden on Henry with a stop sign, the Left 4 Dead 2 frying pan sound can be heard, the M16 Assault Rifle sound from L4D2 can be heard when a guard fires his M16, in Presumed Dead ending.
League of Legends - In IRO the option for "flash" appears while you're in the cafeteria. Not only does it make the sound when you use flash in the game it also has the art and it lets you teleport through walls just like in the MOBA game.
Lemmings- in Fleeing the Complex, if you try to escape through a hole in the wire fence, fail description says "You could use one of those", followed by an image of what very closely resembles the Blocker lemming special ability.
Mario- Super mushroom appears in Stealing the Diamond. It makes Henry bigger like in the games. There is also Luigi's portrait in the same room. Green shell is an option in Infiltrating the Airship. A Racoon Leaf and a Boo from an item block are also used in Fleeing the Complex.
Mass Effect - In ItA, Earpiece Option, the part where Charles said that he hacked into the power grid, and asked what he should do, the display of choices looks like from Mass Effect.
Mike Tyson's Punch-Out - In FtC, Presumed Dead, Henry can choose to fight the big guy with boxing gloves. The scene will play out as if it's Mike-Tyson's Punch Out.
Metal Gear Solid - The call sound effect can be heard in the first option screen of Infiltrating the Airship. The iconic cardboard box used for stealth sequences in the series is also one of the options in Fleeing the Complex.
Minecraft - In Stealing the Diamond as Henry uses a pickaxe in similar fashion to the characters in the game, the exploding mob, the Creeper comes up to Henry. The wall breaks in many cubes, another reference to how everything in Minecraft is made of cubes.
Papers, Please - One of the ending slides for the "Presumed Dead" ending in Fleeing the Complex shows Henry handing his passport to an immigration inspector.
PilotWings 64 - one of the fails in Stealing the Diamond are Jumble Hoppers, which are named after the character Jumble Hopper who jumps just like Henry with those boots. It also uses the music from the game.
Pokémon - Pokéball appears in Stealing the Diamond. When the player chooses it, next scene is actually based on Pokémon games. The Pokémon Missing.no is a glitch Pokémon found on early releases of Pokemon Red/Blue that just appears as lines of code.
Portal - In Stealing the Diamond, Henry uses a Portal Gun and fires it to diamond and on the ceiling, which then crashes on his bridge and leads to fail.
Power Glove - A peripheral that allowed motion control for the NES that Henry tries to use to raise a door.
Sonic the Hedgehog - In Stealing the Diamond, a Sonic water bubble is used to reflect bullets and in Infiltrating the Airship, a Tails robot is used to cross a gap. In FtC, Presumed Dead, Henry can choose Speed Shoes as an option, which is what Sonic wears, and the red spring appears in Ghost Inmate, in FtC, complete with sound effects.
Starcraft 2 - In Henry's Cell, he will have the option to use the Teleporter. When he does this, it will teleport him Protoss-style to a planet where Protoss are fighting other Protoss. Henry will appear among some Zealots, who are preparing to attack an enemy Colossus, and are vaporized. Then a player, Bassen, will tell the other team to leave.
Star Fox - The call sound effect can be heard in ITA.
Street Fighter - Ken can be seen using a shoryuken against Ryu during the desert battle in ItA chaotic ending when the airship crashes.
Super Smash Bros. - The fact that Henry trips when left is selected in Escaping the Prison during one of the quick-time events where he evades two guards is a reference to how characters in Super Smash Bros. Brawl may randomly trip when attempting to run left or right; this mechanic is regarded by many as annoying and infamous and easily disrupts competitive play.
Skyrim - In FtC, Ghost Inmate, Henry has the option to pickpocket Isaac, the menu, Skyrim-styled, will be shown. Henry will surprisingly steal everything without the guard noticing, after Henry took everything, there's a note which tells him he's unable to stand due to the heaviness.
Team Fortress 2 - A TF2.exe icon appears on desktop in Infiltrating the Airship, and a Scout appears when it's clicked in one of the endings. Also, a Soldier's rocket launcher is used to rocket jump in one of the paths. The Sniper appears in Stealing the Diamond on a police chopper, who says one of the catchphrases from the game if Henry fails to choose anything. In the cutscene before choosing the CD in Infiltrating the Airship, the BLU Spy can be seen backstabbing the RED Sniper. In Fleeing the Complex, one of the medals is called "Kredit 2 Team", with its icon being red/blue, just like the teams in the game. It also seems to depict a Heavy class, which would fit as he's Russian just like The Wall complex seems to be.
Telltale Games - Leaving Ellie behind in Fleeing the Complex will give a player a notification saying "Ellie will remember that".
The 7th Guest - In Fleeing the Complex, when Henry uses Earth Bend, the music that plays sounds like the music from The 7th Guest when climbing the vine in the Music Room.
The Binding of Isaac - Monstro's tooth can be seen as item held in pocket of The Wall guard called Isaac (double reference).
The Neverhood - the Liquidificator fail in Stealing the Diamond involves Henry holding a piece of paper without moving at all, just like Klaymen used to read letters in nursery's basement. It even uses the same musical tone. Also song when Henry uses opacitator song Dum Da Dum Doi Doi.
Tony Hawk's Pro Skater - Scores that are shown when Henry uses acrobatics in FtC are the same as in this series.
Worms - Banana bomb is one of the weapons from the series. There are also some sound effects from these games.
LEGO - A LEGO brick is shown in the option Warp which then references LEGO Racers.
Lolwut pear - An art picture of a laughing pear was posted on internet and a lot of people started photoshopping it, later it was known as "Lolwut pear". It appeared on picture in the museum in Stealing the Diamond.
Sweet Bro and Hella Jeff - A flash comic were a guy falls down stairs is referenced when Henry falls down the museum stairs in Stealing the Diamond.
Wheres Waldo? - Waldo can be found as an easter egg in FtC.
Windows- In StD, during the error in the Pokemon battle, it shows errors in Windows 95 style, and the Windows XP Critical Stop sound can be heard in the BSOD. Also, this caused the fail screen to be glitchy. The fail screen had some buttons animated without your cursor on them and the FAIL text tilted. The "Back to Menu" button was glitched.
MLG Parodies- In Fleeing the Complex, in the Convict Allies if Henry is given a sniper rifle, and Ellie is given a Crossbow, Henry will accidentally 360- No Scope Ellie by mistake. In the fail screen, you can click the fail quote to initiate a scene based on Major Gaming League (MLG) videos that are very popular montages on YouTube.
Source Engine - In Presumed Dead, in FtC, Henry can choose Tool Gun as an option, he will input sv_cheats 1, and noclip. The cheats are from Source Engine. Henry will also noclip to escape, in which he promptly got kicked.
TDK - In the chaotic ending of ItA, discs that Wilson can use to solve the chaos have TDK logo on them, same as the logo of the real life Japanese electronics corporation.
YouTube Personalities- videogamedunkey's line "Not even close, baby" is a fail line if Henry fails to pick a choice during the truck chase sequence in FtC. Markiplier and Jacksepticeye (both made very popular commentary videos about Henry Stickmin series) make cameo appearances as prisoners in FtC.