These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Strangely enough, the entirety of the Kin count, with the possible exceptions of Sennir and Laneen, as they only appear in a couple of chapters in-story but they get almost as much, if not just as much attention as the rest of the cast.
Fridge Horror: Preosh's lusus is a whale. The first lusus Eridan was seen to kill in canon was a whale with purple blood...
When Sollux and the Psiioniic talk, the Psiioniic tells him to not get caught, because he 'can't face that again'. He's talking about Laneen- the Condesce forced Laneen to fuck her and the Psiioniic, and the Psiioniic knows that Sollux is his descendant. Not only has the poor bastard been wired into an engine and raped, but it's entirely possible that he'll end up having to rape and be raped by his child... again.
The cell Gamzee was kept in was covered in black stuff, the identity of which was never made explicit. Word Of God in a chat with the readers was that said slime was smoke; the Big Bad pair used to like to take trolls in twos, and there is an oven with a vent leading into the cell...
Condesce, going by her behaviour towards Gamzee, likes them young. She's known GH almost literally since his birth. It's later confirmed their relationship was at least vaguely sexual when they were at the equivalent ages of twelve and twenty. Also, Pyeran is the youngest of the Kin, but Aradia confirms that other victims died too soon to be bound, and GH said in response to a reader question that victims younger than that die too soon; presumably they know first-hand.
Halloween art. Don't see why Humanstuck is scary? Humans raise their offspring from birth.
According to Jade's explorations of the troll web, someone made a video of Eridan during his Anything That Moves phase, probably without his knowledge, and put it on a public porn site.
Sollux is most likely the child of the Psiioniic and the Condesce, but depending on whether she made them fill a pail or not, he could also be the child of the Psiioniic and Laneen.
Look at this ask. The green blood on the Grand Highblood is most likely Lereal's.
It Gets Better: Some readers are put off by the characterization in the earlier chapters, especially if they haven't read "Reprise" and don't know why Gamzee is acting the way he is. This is usually rectified once Character Development sets in and things start being a little less grimdark.
Jerkass Woobie: Gamzee, especially in earlier chapters. He's pretty Ax-Crazy and does some truly horrible things to his friends, but considering what he's been through it's hard to blame him.
Moe: Ganmed and Tsukey are both pretty damn adorable.
Paranoia Fuel: The buildup in Reprise. Described by one reader: "I was reading it and thinking 'Well, this isn't so bad, a little creepy maybe, but I think even I wouldn't do too badly in an environment like... uh... oh... Oh my god."
Ron the Death Eater: Kanaya. While she's still a heroic character, she's much more bitchy and antagonistic than she is in canon, and constantly fights with Karkat when they were close friends canonically.
From her point of view, though, Karkat's risking everything for the sake of the guy who threatened to rape her friends as "punishment" for nothing worse than stupidity and may still decide to kill them all.
Selective Squick: There were children in the Trap, but the warnings page confirms that graphic details of what happened to them will not be shown onscreen, despite the lurid descriptions of everything that happened to Gamzee.
Squick: Entirely intentional, to the point that it requires a whole extra page just for the trigger warnings.
Unfortunate Implications: None of the trolls ever seem to get called out for the fact that Equius and Eridan were effectively kidnapped, forcibly converted to Sufferism, and made to defect against their former allies against their wills. Considering the clear parallels between Sufferism and Christianity, it's not hard to be reminded of some of the atrocities committed by the Spanish Inquisition. Granted, they get better, and it's hard to argue for what they were fighting for before, but...
What an Idiot: Equius and Eridan, admittedly both fairly badly indoctrinated into the Empire's regime, assumed Gamzee's message about his mentor touching him inappropriately was meant as bragging and told him to just keep doing what he was told. Karkat makes a comment about how they would have happily pailed their mentors, and they don't deny it. See above for how well that worked out.