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.
A very early strip has the characters edited to remove their arms, a la several of the Homestar characters.
This strip is a recreation of a Garfield strip made in Make-O Your Own Stinko, with Stinkoman as Garfield and a Chorch on the robot octopus as a bird on a birdbath.
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.
The eighth episode of the Game Grumps' let's play of Strider is entitled "The System is Down".
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.