The character of Equius expresses frequent references to Hussie's previous works, which were a lot Darker andTrollier than Homestuck. His lusus is a reference to Humanimals, he is interested in analysing Furry muscle fetish porn as high art (as Hussie once ran a blog doing), and his arc involves Extreme Doormat submission to a clown character to the point where he simply allows the clown to kill him, referencing Whistles, a story about a clown whose Achilles' Heel was obsessive submission to his ringmaster, to the point of self-mutilation.
In Rose's room, she has sketches of some characters from an abandoned novel Hussie had been writing that served as a trial run for Homestuck in terms of feel and characters. It was a Harry Potter-like story about a wizard summer camp that apparently filled with "Homestuckian convolution", and will apparently never be finished because it is too similar toHomestuck. The Running Gag about characters loudly declaring that magic is not real is also a reference to the book.
There are quite a few references to the main Walkyverse in Dumbing of Age (basically a High School AU to the Walkyverse). For example, in one strip the teacher Leslie jokes that every girl in the Gender Studies class is actually a lesbian. In the main Walkyverse, she is a lesbian. On a less jokey level, there's also Monkey Master and Dexter, a cartoon starring the two villains of It's Walky!
In Raruto Sisepuede, a parody of Naruto Shippuden, Chochimarunote Orochimaru just quits being evil and leaves the lair, after which Kabutopsnote Kabuto ragequits. Now Saskenote Sasuke needs to feed Chochimaru's dog and can't find the fodder, so he asks the members of The Heavynote Hebi for help, but they self-appoint themselves as Saske's teammates. When Saske tells them Chochimaru's gone, they jump to the conclusion that Saske killed him, just as a journalist passes by. Cue Gossip Evolution: just a few hours later, everyone in the ninja world thinks everything about Chochimaru's death and the forming of the Heavy went just as in Naruto.
Someone allowed Sun Wukong to compete in this tournament. No one is safe. Luckily, Tenshinhan looked like Buddha. Guess who eventually defeated the Monkey King in Journey to the West?
During U18 Pan's fight with U13 Kakorot, a gag occurs that goes back to the original series. When Kakorot grabs Pan so she can't use the Kamehameha, she simply directs it out of her feet - something only done before with Goku during the 23rd Budokai Tenkaichi.