In his 79th video, with guest star Sonik, while expressing his flattery at his fanboys (remember, this was his firstLet's Play), he name-drops two other more experienced Let's Players like DeceasedCrab and ProtonJon. Can be considered Hilarious in Hindsight in regards to the latter.
When in Luigi's 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.
His first opponent in the Pre-Gym in episode 3 is named Botan. He then references the character Botan from YuYu Hakusho.
In episode 11, when showing where he can and cannot go in Pyrite Cave, he says "We try to go to the left, and there's some real cool boxes that I'd like to break and take the goodies inside, but unfortunately, I'm not Gordon Freeman."
He often makes Fire Emblem Awakening references to certain parts of the game. Examples include joking about the Lucina Drones changing you into a Lord, referring to Miriall as a mage before saying he's kidding, and one time calls Don Argentis Donny and talks about his aptitude.
Right before heading in to the boss of the Old Clockworks, when Professor E. Gadd says "It's high noon", there's a Freeze-Frame Bonus of text remarking how a friend of Chugga's insisted he make an Overwatch reference. Which Chugga doesn't play, so in this case, the Shout-Out is him basically pointing out the lack of a Shout-Out.
The description for Episode 5 (when Chuggaa was talking about Splat Charger) was just one sentence: "Sniper's a good job, mate!" Takes it a bit further in a later episode, when he says "be efficient", and then follows it up with "and have a plan to kill everyone you meet".
The description for Episode 10 (which covered the Heavy Splatling) references the Heavy. Goes a lot further at the end of Episode 9, in which he says that in the next episode he would "touch Sasha".
The Inkling Boy amiibo featured in Chapter 10 was given the nickname "Purplflurp"
Chugga takes down the cultists of Happy Happyism, who seem to have a special affinity the color blue, in Episode 10. Fittingly, the episode is titled "What's the Use of Feeling Blue?" with "Won't it be grand to get rid of it all?" as the description.
Chugga drops a little Fire Emblem Awakening reference (specifically, he's referencing Vaike) when he goes to give the Fry Pan to Paula:
"I didn't forget, I just didn't remember right away."