Bro's Cool Shades being Kamina shades. John calls them "dumb anime shades" as a nod to this, and Word of God says that it wasn't deliberate at first, but his forum-goers asked him about it and brought Kamina to his attention.
WV and PM being an ex-soldier and a female respectively were both Fanon until Andrew made them canon.
The Pre-Scratch Trolls having more than a footnote in the story come from fans dogging Hussie for information about them.
Rufioh Nitram's name was a prevailing Fan Nickname before his introduction.
Fandom Nod: Many, as Hussie considers Homestuck a conversation between fandom and author.
Fan Nickname: Bec Noir and Jack English for the B2 and A2 Jack Noirs to distinguish them between each other and Spades Slick. A2 Jack is also often called Lord Noir or Union Jack.
"Murderstuck" for the infamous section of Act 5 Act 2 where Eridan and Gamzee lose it, resulting in half of the Trolls getting gruesomely killed off.
Daddy Droog for Diamonds Droog in reference to the fans interpreting him as a father figure for Aradia.
"Cali" and "Uu" for Calliope and Caliborn due to them sharing a body. Calliope herself is often called Callie.
Before Doc Scratch's identity was revealed, fans just called him White Text in reference to his typing style.
Arasia for the Handmaid due to her oriental clothing style.
Bec Blanche for PM, post prototyping.
The carapacians enslaved by the Condesce are often called Famished Ruffians.
Flip Flop of God: Hussie has presented two contradictory views of Sburb: that A) one session occurs in any given universe (successfully anyways) and B) multiple sessions occur in any given universe and indeed multiple sessions can occur on the same planet at different points in time. There's evidence enough to support both sides, but given certain events like the Great Undoing, it seems the former explanation is more correct.
The first page went up on April 13, or 4/13. Since then, the comic has used 413 as an Arc Number all over the place. Given the way Hussie's been writing by the seat of his pants, and that he had originally tried to launch the story on April 10, it's safe to assume he built the arc number around the launch date rather than vice versa.
Also, various anniversary animations have been released on 4/13, on the 413th day, and on similar dates based on the second Arc Number 612 - which itself is a Meaningful Release Date. 612 is introduced in Act 5, which started on June 12th.
The Finale of Act 5, "[S] Cascade", had one of these accidentally. It was originally meant to be released in September, but Schedule Slip delayed it so much that it wasn't finished until the middle of October, so Hussie agreed to hold it off for a few days to match the third Arc Number, 1025.
1025 is the sum of 413 and 612, so 1025 is also a combination of the two previous arc numbers.
And Act 6 introduces a new arc number, 11 11 11 - Act 6 began on November 11th, 2011.
In the Act 6 Act 4 flash, Jack Noir is seen marking off days in his jail cell as time passes for the Alpha session. At the end of the flash, twenty-one weeks and six days have passed (21 and 6, or 612 backwards). That many days after 11/11/11 is 4/12 of 2012, one day before the Beta kids will enter the Alpha session, and that many days before 11/11/11 is 6/12/11.
To elaborate on the "exist within the same canon", the world of the Midnight Crew is the same world as those of the Trolls, who also exist in (or at least communicate with) the kids in the Homestuck world, but are from an alternate universe.
And, to take things even further, the art style and some of the universe mechanics for Midnight Crew suggest that it also takes place in the same universe as the previous MS Paint Adventures comic, Problem Sleuth.
Part of this is explained by the fact that Andrew Hussie exists in Homestuckbeyond the fourth (and fifth) walls, which is apparently between the other universes. It's implied he's been sending Midnight Crew comics to the human universe, Homestuck comics to the Troll Universe, and a sequel for Problem Sleuth to the post-Scratch human universe.
"The year 4 Megapause": On April 14th, 2013, Homestuck went on hiatus due to Hussie needing time to work on the aforementioned game. It returned on June 12th, 2013.
The "Gigapause": On October 17th 2013, Homestuck went on hiatus due to Hussie deciding that it would be best if the remainder of the story was completed and released in one go.
Teasing Creator/Trolling Creator: Andrew Hussie's jokes on the fans are legendary. Many of his self-inserts into the story are there solely to make fun of fans who were upset over certain plot developments. He also likes to throw Red Herrings into the plot liberally and then subvert the audience's expectations. He further has a habit of building up to a reveal or climax, and then abruptly cutting away to some other random part of the plot for a while, knowing that this annoys the readers to no end.
Hussie had planned Heroes of Light: Strife, an epic animation for round two of the battle between Grimdark Rose and Bec Noir, as well as the battle between Vriska and Bec Noir but was cancelled, as explained here:
Hussie: The planned animation would have been a major escalation in production value. The sophistication of the animations has increased over time, and part of the point of this for me is to keep pushing the envelope, but there are limits to how far you can go. It's good to keep pushing and find your limits and test them, but realistically you'll have to pull back at some point. Because that is what a limit is. A line between something you can do, and something that is literally impossible.
I'm not saying the animation I had in mind was impossible, but it was approaching scary territory. I just made a judgment and decided it wasn't worth the energy, all things considered.
So instead, the fight is shown in an abridged, narrated, slideshow-like format. While many fans did not like this and preferred epic flash animations, some admitted the "abridged slideshow" at least got the job done.
Earlier, Dave's Inventory Management Puzzle was going to lead up to a hashrap battle between Dave and Bro. Hussie decided not to go through with it - and this is actually lampshaded by Dave after the actual Strife with Bro. Much later in Act 6, Hussie did manage to do a rap battle using the Inventory Management Puzzle, thanks to Dirk and Squarewave.
After Problem Sleuth finished, Hussie thought about doing a Midnight Crew adventure before starting Homestuck. Though this never came to be, they did ultimately became important characters in the comic and got their own Intermission.
Homestuck was originally going to be done entirely in Flash, as in the Beta version found here. This was abandoned as Flash was too much work.
Word of Gay: Kanaya is confirmed by Word of God to be gay: although trolls do not have a concept of sexual orientation, maleness is a deal-breaking turnoff for her.