When Tre finishes his Replay, the sequence following it partially resembles the scene in Harry Potter and the Deathly Hallows where Harry goes into limbo after dying.
When the gang contemplates what to name the Challenger that eventually becomes The Dynamo, the names "Elaine!" and "The Ecto-2" are bandied around.
Lampshaded by Nora right after, too.
Nora: We're fugitives, not the Ghostbusters.
Marceline Hughes shares a first name with a certain vampire queen, though it isn't made obvious because in most cases she's called Marcy.
Cale McMillen's named after Cale Tucker from Titan A.E..
Allie's a badass action girl with the last name Silverburgh.
The name of the second act of Stuck at the Galleria is "The Duck Hunter", a reference to both Duck Hunt and Spy Hunter.
Most of Lyle Terry's digital art he posts on his Tumblr is usually based on Homestuck panels.
"Young Folks" by Peter Bjorn and John is referenced at the beginning of Tagged, and Tre namedrops it, for that matter.
For that matter, the soundtrack playlist for Episode One includes songs by Skrillex and deadmau5, both of which are referred to in the book (though not entirely by name).
Another one that started as an odd coincidence: By his third outing as a main character, Tre ends up having ridiculous hair, parkour skills and an affinity towards using a sword that isn't actually a real one. Same thing with Fancy Pants Man.