- Several comics have Alt Text that bring up Meta Knight's Game-Breaker status in the Super Smash Bros. Brawl competitive community.
- #50 is done nicely In the Style of Bill Watterson, with Kirby as Calvin and Dedede as Hobbes.
- One memorable strip actually had a comment saying that Matthew's nerdiness had reached new heights (even though the reference isn't that hard to grasp).
- #104 is a strip about Snake goofing around in his cardboard box. The author's note?Next up, scientific progress goes “boink” as Snake uses the box to clone himself! note
- How the King Stole Christmas (Part 2) has King Dedede do an impression of CD-i Link's infamous laugh when the lyrics say "the only game YOU deserve is on the... Philips CD-i!"
- In 125, Baby Mario's prattling ends in the second panel with "now I know how a meatb..."
- And from the same episode, in 205, Luigi strikes a rather familiar pose while mentioning Yoshis who call him "mama".
- Also in the above strip, a middle-aged witch girl appears, but people likely won't know who she is until she shouts...
- Captain Falcon evidently commutes with Futurama's Hermes Conrad, as well as Dwight from The Office (US). In The Rant, Matt explains that he put "hints" as to who they are supposed to be in each of their cars (Hermes has an air freshener that looks like the Planet Express ship, and Dwight has a brand on his steering wheel that looks like a beet and has the Schrute Farms initials).
- Pichu's evil expression here is a direct copy of the Grinch's. The Alt Text expands by providing the commentary during that scene in the special.
- #190: "Where's Waluigi" is a parody of Where's Wally?. Wally himself is hidden in the comic: he's hiding behind Bowser Jr.'s painting.
- Eggplant Wizard and King Hippo are standing next to each other, referencing their role as a Bumbling Henchmen Duo in Captain N: The Game Master.
- The conclusion of the "Snake in the Grass" arc has Solid Snake assuming the same position as a certain unconscious, naked guard from the first Metal Gear Solid.
- Teddie makes an appearance in strip 249.
- #250 references four different comedic cartoons, plus the Kirby anime.
- #300 has Ganondorf kicking over a chessboard in a very Gaston-like context and fashion.
- The alt text for 310 - The Casanova pulls a Russian Reversal of the old Mudkip meme, fitting with the comic:So I heard Mudkip likes you?
- In Part 10 of "Cocoon Academy", when Pinky wakes up in the nurse's office after absorbing some of Dark Matter, the first thing he says is "Mirror... MIRROR!!!"
- The creator's comments for strip 235 say "LENS FLAAAAARE"
- The Alt Text for this strip discusses what DK's Giant Punch would be like if it were a Magic: The Gathering card.
- The sound made when Peach falls into the grass outside Bowser's Castle in "The Captive Princess" is "POOMP", which is the same produced when you land a huge jump in Mario Kart 64.
- Similarly, the Gooey Bomb goes off with a "BOMB" when Meta Knight accidentally stabs it.
- For whatever reason, several of the "Waluigi in the Family" strips are named for levels in Teenage Mutant Ninja Turtles: Turtles in Time.
- Amaterasu had a quick cameo in an alternate ending of Sun's Song, Part 3, fixing the mess Link had made.
- The strip "Tired" has a tired Mario hallucinating about going to his bed, among various clouds, with the moon smiling at him, all while driving back home.note
- The author's note for this comic starts off with a reference to Phineas and Ferb.
- In this strip Pit and Mega Man recall their time in the Captain N: The Game Master cartoon... although Mega Man wishes he didn't.
- In the same strip, Jigglypuff (now a Fairy-type) is seen with a wand, a floaty-crown-thing, and a copy of Da Rules.
- In the 500th comic milestone video, Mega Man, homeless and looking for work, periodically alters his message on the board behind him to say, at various points:
- "Game unplugged, please help!"
- "C'mon, Roll got to hang out with Jun the Swan"
- "and Zero is partying with Spider-Man"
- Speaking of that video, it ends with a cartoon version of the opening of Mega Man's trailer of Super Smash Bros. 4.
- Speaking of Roll and Zero, Mega Man bumps into Ryu, hoping to join him in his next game. Ryu awkwardly reveals that they already got a different Mega Man, one from the American Box Art.
- Hilarious in Hindsight, given how Ryu was eventually added as DLC.
- In the Mega Man 3 party scene, his allies Pit and Simon Belmont from Captain N: The Game Master can be seen, plus Samus from the comic book adaptation who replaced the third party characters for copyright reasons.
- His name is Yoshi, and he loves you.
- #563 has Kirby turn into Sterling Archer upon consuming an archer. The Alt Text states that that the Bell ability lets him converse with candlesticks, clocks and teapots.
- #574 ends with a clever reference to the ending of Duck Amuck.Bowser: Ain't I a stinker?
- And the Alt Text pun:
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