Homestuck fandom has the popular "bloodswap", an Alternate UniverseWhat If? fic where the alien trolls have different blood colors than they do in canon - blood color being used to determine their place in the Fantastic Caste System and what Psychic Powers they get (if any). The most well-known bloodswap fic is Red Dead Virgo. A few other fanfics (including RDV) do something similar with the human characters where they are raised by different people than they were in canon.
A variant keeps the bloods of the characters the same, but reverses the social standing of the hemospectrum such that former rustbloods are in charge and seadwellers are the lowest castes.
Perhaps the most common form of fanfic for Homestuck (or at least the most common fan-adventure), are the ones in which a completely new group of players (human or troll) plays Sburb. A Sburb session is a ready-made framework for a story and canon that the main characters weren't the only humans to start a session (though it's strongly implied that all other human sessions should be doomed to failure and Word Of God has declared that the trolls were the only session for their species). Only very rarely does someone actually bother to invent their own race of aliens, despite that being far more likely canonically, and not everyone succeeds in putting a big enough spin on the premise to make it worthwhile.
Fan-Adventures consisting of the cast of other shows are also common.
Life after The Scratch is another big one. These generally revolve around the characters remembering or trying to remember their past or alternate lives. In many stories the trolls are turned human somehow.
Fake FAQs for Sburb, based off Rose's FAQ in canon. Originally, many of these fics treated Sburb and the events of Homestuck as a fictional video game that people were writing strategy guides for. Fake FAQ fics then went dormant until they were revived by the story Sburb Glitch FAQ, which eventually started a Fan Verse.
"Petstuck" AU stories, in which the trolls are animals kept as pets by rich humans, are relatively common. The majority of them begin with a normal person finding an abandoned troll (cardboard box and rainstorm optional), taking them home, gradually getting them to open up and trust humans after years of abuse by their evil former owners, realizing that trolls are actually sentient after all, and attempting to get them recognized as more than animals by society.