Koko Hekmatyar in the English dub of Jormungand, makes a quick reference to Trogdor by saying if she was a dragon she didn't want to do any burninating during the episode "Dragon Shooter phase.2".
The Mitchells vs. the Machines: The part in Dog Cop where Monchi "drives" a police car (the far shot of the car is just a toy on a stick) was confirmed to be a homage to Dangeresque: Puppet Squad - The Hot Jones Hijack.
During the Episode Hell Week, Mary is shown working at her computer with a Strong Bad Figurine sitting on top of it.
In the episode Flying High, a Trogdor Black shirt is seen on a table.
In two unknown episodes, the team makes two cakes to resemble Trogdor and Pom-Pom.
In the episode Pandamonium, in the course of fooling around with Geof after the principle work on building the Kung Fu Panda cake had been finished, Duff exclaims "Are you asking me for a challenge?!" before karate chopping a large stack of sheet cake.
In another episode, Mary is shown wearing a Teen Girl Squad T-shirt.
In a season five episode of Angel entitled The Girl in Question, Spike and Angel visited Buffy's apartment and instead found Andrew, who was wearing a black Strong Bad t-shirt. Later in the episode, Andrew wore the same Strong Bad shirt with a pore strip plastered on his nose.
In Chapter 2, the three members of the music-themed rebel group call themselves the "Sweet Cap'n Cakes", which is one word off from Strong Bad's crazy cartoon Sweet Cuppin' Cakes. One of the members plays a song very similar to the one that Casio Head Strong Bad plays, which is called "When I Get Mad I Dance Like This" on the official soundtrack.
One of the minigames requires you to play an arcade game. Once you complete it, a vector-style explosion similar to the one from video games.
Final Fantasy: A guy outside the Hellfire Chasm warns that any trespassers will be burninated.
The author of this strip mentions it was originally made to be posted on the Homestar Runner fan wiki's message board.
This strip makes reference to Homestar Runner's "buttdance" (along with the rejected character Homeschool Winner). The reference was later clarified in the author's notes for a later strip.
In this strip, Jon tries to use his answering machine (actually Marzipan's old answering machine), which tells him he has no messages in the same manner as an Easter Egg from the King of Town cartoon.
In Nostalgia Critic's review of Ernest Scared Stupid, he mentions that Trantor doesn't seem as cool as Trogdor, which is followed by a clip of his revival scene with Trogdor pasted over him while his theme plays in the background.
During the episode "Bloo's Brothers" a Bloo clone that looks very similar to Homestar appears very briefly. This version reappears in a mini-game in "Big Fat Awesome House Party.
The ending of the episode "A Sight For Sore Eyes" is very similar to Old Intro 2.
In "Duchess of Wails", there's an orange imaginary friend that looks like Trogdor.
In "Infernal Slumber", both Bloo and Goo talk about "killer Pooooooosssssssumssss", dragging the word out much like in Teen Girl Squad Issue 3, (Goo pronounces it exactly like Strong Bad).
In "Squeakerboxxx", one of the prizes is a clock that looks exactly like Strong Bad's, complete with 12:00 as the time.
In the episode "Land of the Flea", Frankie apologizes to Eduardo and says, "We're sorry, for reals this time". Also in that same episode, one of Eduardo's fleas holds up a news paper and says "Eggs tree, eggs tree", much like that of Homsar.
At the end of an episode of Maya & Miguel, when they interview real people, a kid was seen wearing a Strong Bad hoodie, though this is barely viewable because the picture is blurred out.
The Unikitty! episode "Film Fest" caps off Unikitty and Puppycorn's film with an end card that consists of "It's over!" drawn on a piece of lined loose leaf paper, in reference to every ending of the Teen Girl Squad episodes.
Robot Chicken: One sketch has the government raid Free Country, USA due to mistaking Strong Bad as a sepratist enclave. Several characters die in the ensuing chaos.