Every time the boulder rolls down the path in DK's Jungle Adventure, Jon sings (or rather "duns", or "dunts", according to Chuggaa) the Indiana Jones theme, in reference to the famous scene in Raiders.
References are often made towards SlimKirby, notably his Anti-Peach Song while, naturally, they're playing on Peach's Birthday Cake.
The biggest reference, when Chugga won by one coin (In SlimKirby's Mario Party 5 LP, he lost by one coin):
Chugga: I got something to say, and I'm gonna get real close to the mic to say it. (Beat) Suck it, Slim.
Whenever they play the minigame Crazy Cutter, they read it in the same way the in-game announcer of Crazy Taxi reads its title. (They once did the 'Yeah Yeah Yeah Yeah Yeah' for the opening music. [What I Want by The Offspring])
Tim quotes the opening to U2's "Vertigo" when he collects his first star in Jungle Adventure.
A couple of references to The Legend of Zelda CDi Games from Chugga, including stating that "Bowser and his minions have seized the island of Koridai" in Wario's Battle Canyon.
About 2 minutes in to Bowser's Magma Mountain Episode 1, Jon starts talking about Mumbo Jumbo from Banjo-Kazooie's incantations and how Maffew from Botchamania talked to the guy that did the soundtrack and said that everything Mumbo said was a dick joke.
After everybody determines their turn order in Mario's Rainbow Castle and shouts what they got, Tim spouts off some numbers of his own.
When everyone but ProtonJon was in a bubble at the end of 2-4, right before the flagpole he put himself in a bubble, mirroring what happened in the Freelance Astronauts' LP at 8-1.
Jon: Thanks, Maxwell!
In episode 16, Jon immediately recognizes the level as the same one where Ferr sang sea shanties while screwing around with the controllable platform in the Astronauts' LP. After NCS accidentally moves the platform into a lava pillar, killing all four of the players, Jon even comments:
From Episode 12, Jon makes two references in quick succession: "All right, everybody, welcome back to American Gladiators! This time the red team, green team, blue team, and yellow team will be fighting it out against The Aggro Crag!"
When someone else gets something wrong, Chugga is fond of shouting "WRONG!" in the same way as Lex Luthor in Superman Returns, and then following it up with "LEX WINS!" as a reference to ProtonJon's LP of Superman 64.
In the intro to Episode 13, Tim quotes the Gregory Brothers' Charlie Sheen "Winning" song, but says "I was banging seven-pound rocks" rather than "seven-gramme rocks", prompting Jon to point out that that much cocaine would kill a man.
Episode 17, after fooling around with Olimar's name:
Emile: Polymerization! We're playing Yu-Gi-Oh! now.
Jon: I play this card in defense mode! I play this Pikmin in attack mode! I get on this button in attack mode!
Emile: You came back from the dead just to play a card game with me.
Jon: I am lying down in defense mode.
During the later episodes that were filmed at ProtonJon's house, Jon started showing Chugga and Tim Clone High. As such, the rest of the LP contains tons of references to it, including many JFK impersonations.
At the beginning of Episode 3, Jon says they're having a pool party in Raisin Ruins. Jon then attempts to kick Chugga out, saying that "Only Aquabats are allowed at this pool party!"
In episode 3, the guys start discussing what Meta Knight might actually look like under his mask. Jon says he likes the Brawl in the Family interpretation of Meta Knight being just another Kirby who got coloured blue and lost some of his powers.
When Chugga!Kirby gets Snow Bowl for the first time, Jon deadpans "I don't wanna play Katamari with you anymore."
When Tim gets sent to the volcano (which Jon dubs as being hell) he starts singing the Irving Berlin song "Cheek to Cheek" with appropriately modified lyrics: "Hell, I'm in hell, and my heart beats so that I can hardly speak..."
In the Globe Trot game, when the camera is focused on Africa Tim sings a bit of Toto's "Africa".
During the Jumbo Jump ski game in Spin Off, Jon sings the Sonic drowning theme.
After noticing their avatars are wearing bow ties, Jon keeps making Doctor Who references, much to Chugga's bewilderment.
Tim sings "Kryptonite" by Three Doors Down ("If I go crazy, then will you still call me Superman...?") when they play a game that involves flying through space in capes.
Chugga says he's in the 700 Club (Pat Robertson's televangelist program.) He and Jon lampshade it: "700 [points]! I'm in the 700 Club — I'm referencing that?" "Wow, I am surprised you referenced the 700 club, of all things."
In episode 2 they all make puns on things happening to Chugga's "Moustachioed Shark" avatar: when he gets covered in tentacles they call him Sharktopus, when he gets covered in brown sludge they call him Sewer Shark, and when he has trouble jumping Lucah references Jumping the Shark.
In episode 4, when they play a level called "The Darkness", Tim sings "I Believe In A Thing Called Love" by the band The Darkness.
In episode 5 there's a segment where they have to stick stickers on some ducks in the background, but they have to time it right with signal lights coming on or bombs drop and blow them up. When Chugga doesn't get it right and is killed, Jon says "You chose... poorly".
Chugga starts humming the boss music from Sonic the Hedgehog 2 in the final boss fight, as he says it reminds him of the final boss from that game...which ironically had a different, unique, theme to the regular boss theme that he's humming.
New Super Mario Bros U
The description for Episode 2 says: "The sequel to that one intro!" So what does Chugga sing this time? The Flintstones. But unlike last time the rest of the guys were OK with this.note For extra points, Chugga didn't even make the lyrics, this guy did.
Timstones! Meet the Timstones! They're the modern, Runaway Fa-mi-ly! From the Mushroom Kingdom, Come the friends who need to L to P! Now Let's Play, with Jon and the other three! He couldn't even upload a bee! When you read our fanfics, You'll Have a Gay Old Time! ...But you knew that already!
The look of the thief enemy from episode 4 is compared to a Rabbid from Raving Rabbids.
Appropriately enough, the official name for this enemy turns out to be Nabbit.
In episode 6, when all four of them are in their small forms, Chugga refers to them as "Mario Babies" and sings the Muppet Babies theme song.
In episode 9, Tim quotes the 'Asshole' lines from Spaceballs when Josh calls the others assholes, and later when discussing the P-acorn, he quotes The Angry Video Game Nerd saying "why is there so much P in this game?" (then meaning Super Mario Bros. 3).
Jon: Well, I guess it's Mario Party and I'm always Mario, so I guess I gotta be Mario, right? TOO BAD.WALUIGI TIME.
In the first part of Deep Bloober Sea, the guys play The Beat Goes On, where the buttons involved (A, B, and Z) have to be pressed in a certain order; after the game goes on long enough and the button input order gets increasingly complex, Tim quips "Abba-Zabba, you my only friend."
In Part 4 of Spiny Desert, Jon is fresh off losing all of his stars to Peach in Chance Time and is sorely depressed. When the group is about to play the minigame "Awful Tower", he glumly remarks that, while they're playing, that "Everybody's hating Waluigi". Hearing this, Tim and Chugga start singing "Everybody, everybody!"
In part 2 of Woody Woods, Chugga references the theme tune from Mr. Ed.
In part 1 of Creepy Cavern, Chugga compares the look of the background in the golf minigame to the Hill Top Zone from Sonic the Hedgehog 2 and then attempts to sing the zone music.
Part 6 of Creepy Cavern has Tim initiating the second Last 5 Turns ceremony of the game with his Wacky Watch. When the guys note how funny it would be if this doubled effects of the last 5 turns, like how many coins duels are worth, Tim becomes the host of a round of Family Feud, with Jon even joining in as a contestant.
Tim: Dollar values are doubled in this round, Top 6 answers on the board...
A very obscure one from Jon in part 7 of Creepy Cavern: when Mario gets 668 coins, he references the cancelled sequel to Good Omens, which would have been titled 668: The Neighbour of the Beast.
In the duel map "Pipesqueak", when they play the minigame "End of the Line", Tim starts singing the song of the same name by The Traveling Wilburys.
In "Blowhard", when Jon and Chugga keep counting the spaces they can move to figure out where they'll end up ("1, 2, 3, 4, 5...") Tim promptly starts quoting the "that's the stupidest combination I've ever heard!" exchange from Spaceballs, and Jon replies with President Skroob's line.
Several times in the duel maps, whenever Chugga and Tim play "Fowl Play", Jon always commentates In The Style OfRocky's trainer.
New Super Luigi U
At the start of episode 2, Chugga does the by now traditional cartoon theme song parody...this time it's Runawayniacs.
Later in episode 2, Chugga briefly sings the title line of "So Happy Together" by The Turtles.
In Delfino Plaza, after someone lands on Chugga's Tax Office, Tim starts quoting Prince John from Robin Hood and mimics his affected laugh.
In Delfino Plaza, Super Jeenius references the distinctive way JoshJepson (not present) read out a Rayman dialogue box ("Don't be discouraged, you can do it!") in his famous "Oh my God what was the heck was the what the what the what?!" clip.
In Delfino Plaza, Chuggaa quotes Persona 3's "Junpei's Believe It or Don't!"
Chugga: (just defeated a monster and earned a trap from it) Hey, it's a trap! (fade out to the map, where Khan's Castle is nearby) KHAAAAAAAN!
Chugga and Jon reference All Dogs Go to Heaven in episode 5 when they note that the priest in the Vatic Temple is an anthropomorphic dog.
Jon does a rather good Dalek impression in the same episode when the Robo-Sassin says "EXTERMINATE!"
Whenever the guys fight a lizardman enemy, Chugga will eventually make references to Ed, Edd n Eddynote A season two episode in the show has Double D also being labeled a lizardman.
Chugga thinks one of the town mayors looks like Uncle Pennybags from Monopoly.
At the start of Part 1, Chugga references both Pokemon and, a couple of minutes later, Xenoblade. Funny if you've seen ProtonJon's stream where he accidentally polled his viewers on whether Chugga would mention Pokemon or Xenoblade first the next time they met.
Right after the above, Chugga starts to go on a tangent about how modern series take the term alchemy out of its original meaning; Tim sneaks in a quote from Fullmetal Alchemist, which Jon calls him out on.
Part 2: Chugga reacts to an impressive bounty on Jon's head by stating he just needs to take down a few enemy bases to be worth "a hundred million Beris!" Jon confuses it with the Bells from Animal Crossing.
In part 4, Tim and Chugga duke it out over who gets to control a city. When Tim wins, he decides to prank Chugga by changing his hairstyle to look like poo, which in turn leads to Chugga hoping the hairstyle will look like Poo's ponytail.