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 Slim Kirby, 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 Slim Kirby'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).)
In Mario's Rainbow Castle, episode 5:
Jon, reading what Toad is saying:: But now, there's not a rainbow to be seen. Yes, it is sad. I wonder, can't we go back to the past? Chugga:To play the shitty games that suck ass?
Jon: Wario is really bad at fighting ghosts, he's been possessed like three times. Chugga: He's definitely no Raymond. Jon: Well, Everybody Loves Raymond.
A couple of references to Legend of Zelda CD-i games from Chugga, including stating that "Bowser and his minions have seized the island of Kordai" 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.
They reference the Freelance Astronauts' own Let's Play of the game, in particular their Running Gag of honking a 'fail horn' every time someone has to use a continue.
When everyone but Proton Jon 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:
When Chugga is the only one with a propeller hat, it's agreed that they need him to survive long enough to get the Coin, and thus can't try and kill him. Cue "I'll get you next time, Gadget!NEXT TIME!"
Shortly afterwards, while trying to time a tricky propeller hat jump: "Do it now! GET TO THE CHOPPA!"
Possibly unintentional: At 24:19 in the fourth episode, Tim says: "Jon's a homicidal maniac".
In the sixth episode, Tim is just getting the hang of the bubble mechanic, and hits the wrong button during their run through the castle. Amid the good-natured ribbing, where the others keep telling him that he came close, but didn't quite manage it, comes the line "Well you see, it disappoints Pokémon if they are photographed from behind..."
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 Proton Jon's LP of Superman64.
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.
In Episode 15, Chugga comments that he bet his soul in a card game...achildren'scard game.
Both DragonForce and Foo Fighters get mentioned in Western Land, namely "Through the Fire and Flames" and "Monkey Wrench".
In the Western Land map, Tim can be heard quietly singing Bon Jovi's Wanted Dead or Alive to himself.
Kingdom Hearts got brought up during Western Land, which prompted Jon and Emile to discuss various aspects of the game. Specifically the Gummi technology.
More of an internal shout out, but during Horror Land, Chugga pokes fun at Jon's 'Mario's Wacky World' LP. Specifically, Death Water (and Death Water's son, Led Zeppelin).
Chugga: Does Dizzy Dancing have a son that's a whole band?
Chugga takes a Warp Pipe on the left side of the Bowser Land board and ends up on the right path in front of the Star, prompting:
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."
