The first one was made in Part 5 of the Prologue after Bowser tells Peach that he can grant wishes.
The second was made in Part 2 of Chapter 2 after running away from a couple of Clefts. After that, he mentioned how the show isn't as good as their early episodes.
Some of his Pokémon from this and other games (see below) are references to different things. For example, his Venusaur is named 'Bulbapedia', and his Persian is called 'Meow Mix.'
In the beginning of the game, when Peach tries to object in the Kangaroo Court Mario is in, Chugga also shouts Objection. At that point, the Ace Attorney Objection sprite shows up.
In the first episode, while going over Star Chips, he almost mentioned fighting Pegasus upon getting enough.
When Luigi is killed from lack of gravity, he flips around while that is happening and Chugga mentions Luigi undergoes death by breakdancing in one episode.
Whenever Chuggaa needs to scatter the comets to unlock new mission, he calls the luma who does this, the Ned Flanders of the galaxy, because of that fact that the luma says "Snack-a-diddly-doo!"
During one the Purple Coin missions, he yells "Gah, I love being purple!", referencing one of Patrick's lines from the SpongeBob movie.
He messes around with the Pikmin with bomb rocks when something goes wrong he says YOU FOOL!
He mentioned Electrical Beast and wondered what would happen next in his MinecraftLet's Play. He also predicted that the Minecraft LP would be setting up for the Super Mario 64 Episode 60.
When in Luigis Mansion He encounters Toad obsessing over having dropped something in the toilet and then talking about flushing it in graphic detail, he comments that Toad sounds like NintendoCapriSun.
When the Great Fairy appears, he goes "And now, we meet TIM, HIS WIFE!"
He can also be heard quietly singing NintendoCapriSun's "Take A Dump On The Toilet" after a cut.
After accidentally brandishing an empty bottle, he says he's "reminded of a certain NCS quote.''
Opening Episode 47 with a bit of a parody of how NCS would be so used to saying "Welcome back to The Legend of Zelda:..." that he would open OTHER LP's with "The Legend of Zelda"
"Welcome back to more Super Mario Legend of Zelda Majora's Mask!"
When rolling in Goron form, he sings the intro from Rawhide ("Rolling, rolling, rolling...")
When he first gets the Elegy of Emptiness, he yells, "Don't drown!"
When confronted with an enemy called Marc, he says "Oh hai Mark!"
After defeating Victor of the Winstrate family, he tries mimicking Uncle's "AIYA!" and outright mentions the show's title. The show gets another reference when he's playing Mario Party 3 with Jon and Tim in Creepy Cavern.
