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.
Rather few, even in the "alternative lifestyles" department that most authors would parody or make fun of. Jeph once wrote a three-paragraph explanation apologizing to polyamorous people because of some negativity towards a strip where Tai had problems with the concept, and they're a group nearly everyone else mocks freely. Some of the strip's few real acceptable targets include the slutty (Raven is a fool, despite her Ethical Slut explanation, and Sven is shown as a sex-obsessed cad and man-whore), hipsters (especially ones who take themselves too seriously), indie snobs, and stupid people. The gang (and Jeph) use the word "retarded" a lot, but that's a rather realistic depiction of people in their 20s, and that word gets a pass from most.
Sven may write Country music, but Jeph and every character that comments on it do so negatively. Including Sven himself.
Marten isn't a "Nice Guy", but a spineless coward who is emasculated by the emotional and physical bullying he suffers from the women in his life. It probably started with his mother and got worse with time. He apologizes for anything he thinks might be offensive to anyone, and is so worried about offending someone that he will pre-emptively change the subject or be defensive about a subject he recognizes could cause him to say something 'offensive'.
Marten can also be seen as Straight Man or perhaps a non-dying Decoy Protagonist who isn't supposed to stand for one thing or another. His emasculation and New York Times-esque move to neutrality and centrality is the result of being assigned the role as the anchor to the entire cast. Were he to move one direction or another of his own will, or were he to have a breakdown, the entire cast would be torn asunder.
He also appeared relatively unconcerned when Faye just told Angus about her issues after all the hoops she made him jump through from the start of the comic that also wrecked any chance of a relationship with her. He actually showed more of a reaction to the revelation that Faye hadn't told him what the secret menu was.
A strip by the author dealing with Marigold's first date with Dale delivered a rather heavy handed message that it's perfectly fine for women to have sex when they want, and that it doesn't make them a slut. Rather than having this revelation passed through revealing moments of characterization, it's simply delivered in a blunt single text bubble that feels a little like the author not the character is speaking. Granted, it's completely true.
Some of the political correctness regarding LGBT issues come across as this. Characters go so far out of their way not to offend LGBT characters that it across a bit unnatural.
Faye and/or Dora. There's a large contingent of the fans that love pretty much everything Faye does and still seems to hate Dora for "stealing" Marten from her, and will basically call for anything up to and including her death or being written out of the strip for evils such as not trusting Marten. Meanwhile, a rather smaller group would point out that if your boyfriend had lived for months with a girl he was hung up on, the girl was the one who said it wasn't going to happen but continued to live there, and when it came time for you to move in with said boyfriend he actually argued for allowing his old flame to keep living there, you might just have a right to some trust issues.
Tai. Some fans simply see her as a free spirited and independent young woman whose bluntness is simply because she likes to speak her mind, as well as a great relationship partner for Dora. Other fans consider her to be an unrepentant jerkass, who despite being Marten's friend, never felt to hide her clear attraction to Dora while they were together, immediately tried to hook up with Dora afterward they split up (but stopped when she realised how jerkass it was). Later, when with Marten's support she attempted to properly hook up with Dora, she seemed content to force Dora into a relationship... and it worked.
And when she meets Jim, the bakery owner who previously had an interest in Dora, Tai gets jealous and convinces Marten to try to set Jim up with his mother.
Claire. Yet another boring female character in a comic that needs more characters like humans need bullets in their brain, built solely for the most extreme level of Pandering to the Base seen yet in QC, or another brilliant way for Jacques to introduce more LBGT characters into 'mainstream' web comics.
Strip 1135 features Dora, Tai, and Marten with random mustaches for Cinco de Mayo. Jeph alluded to it on Twitter and forgot to mention it in the daily commentary, so many people had no clue what was up with that.
Pintsize tries to invoke one for strip 1337, but it mostly falls flat. Later, this fancy dress incident occurs, which seems like it must be a BLAM, except they still have the suits in the next comic...and then this happens.
Claire is moving into this territory as well, considering the amount of positive feedback Jeph has received so far for her.
Fan Nickname: The line often gets blurred between a fan nickname being adopted in-universe by the characters and in-universe nicknames being picked up as second nature by the fans. "Hanners" is probably the most commonly-used one both in and out of the comic.
Faye. Jeph comments on this in a newspost within the first couple hundred strips; he specifically says that she really isn't fat, but she has a bad body image, partly because everyone she hangs out with is skinny.
Misaimed Fandom: Apparently TV Tropes writers. Based on Jeph's twitter (Sep 4th, 2009) and news posts on the comic main page, he was annoyed about Hanners/Marigold Les Yay shippers, poking fun at it in this comic. Of course, he also stated that this page is like "every idiotic comment in his forums on one page". Some writers take this website better than others.
Giving into his misaimed fandom led to his Creator Breakdown, when someone on Tumblr sent a butthurt comment to his blog ranting about what Marigold looked like in the bikini, that completely misses the point of Marigold's entire character. She has self esteem and body issues even though her body shape is pretty much identical to Faye and the other curvy girls in the comic.
When Sven sleeps with someone else and then says he was never dishonest with Faye, everyone acts like he cheated on her in a committed relationship and is a huge monster. But Sven is absolutely right... he was up front with Faye about who he was and what he was likely to do, and she was the one who insisted they weren't really in a relationship and that it was purely sexual, resisting all his attempts to make it something more. Faye wanted all the benefits of a monogamous relationship without any of the responsibilities (including the emotional responsibilities), but Sven is still berated like he was at fault for not treating it like a real relationship.
And he has since reappeared! Although Hanners doesn't quite believe it.
Unfortunate Implications: The assorted robots are intelligent beings who are bought and sold as property. Probably best not to think about that too much.
Said robots are perfectly fine with having no civil rights because that also means no legal responsibility for their actions. Given their penchant for wacky hijinks and property damage, they may have made the right choice. Also Clinton's questionnaire asked about a bill trying to be passed to give sentient life equal rights so obviously it's happening but so far in the background we don't hear about it.
Author's Saving Throw: In the blogtext for strip #1996, Jeph establishes that they aren't really bought and sold, but rather it's a voluntary contract which the robots can break at any time. The instances of people abusing the robots without their consent still come off a bit creepy, but this is progress.
HANNELORE. You just want to hug her, except that would only distress her more. Her childhood carves her Woobie status in stone. Apparently she spent a lot of her childhood freaking out, sedated, and completely crippled by her neuroses. Seems to be coping better nowadays, though.
As the strip has its source of humour and drama from cruelty to characters, everybody has both their moments as the Butt Monkey and as the woobie. Marten specially, before he and Dora got their break. As Jeph put it on the author's comment on this Marten-and-Dora-are-Woobies strip: "Awww! Poor Dora. Poor Marten. Poor Mieville, not getting petted by poor Dora."
And then in this strip, we see that, despite anything seen around the whammy strip 500, Faye still loves Marten platonically, and the mere thought of him moving scares her to death. You know you want to hug her.