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.
Also while on the topic of Elliot, is he really unaware that Justin has feelings for him, or is he aware and deciding to not confront Justin about it? There are several arguments you could make for either side, as well as reasoning as to why Elliot would act like that ... however, in lieu of the fact that Justin may or may not have just gotten over his crush off-screen, we may never know for sure what Elliot's stance on this subject was.
Arc Fatigue: Utterly infamous for this. Storylines can go on for years in this comic, despite only taking place over a few days. Only about three or four months (not including flashbacks) have passed despite the comic having been around since 2002.
The "Grace's Birthday Party" storyline is a particularly egregious example. Between the Arc Fatigue and the Schedule Slip, the events of a single evening took sixteen months.
Has gotten much better since updates have increased.
The New and Old Flames portion of Bringing Silly Back ran for one month shy of a year. Add in Indiana Elliot, Hammerchlorians and the two small T-Minus entries and you have an arc that ran for just short of a year and a half real time.
Death Sentence had a bad habit of dragging along; not to mention the central premise was flawed to begin with, with Grace and Raven outright admitting it would probably be kinder to simply kill the boar, considering they're ecologically damaging and huge pests. Though given the eventual reveal that Rhoda is another person empowered without her knowledge, it's really a matter of mileage with this one. While it can be argued that it dragged a bit, Grace and Raven openly communicated about magical stuff, and it's clear that ANYONE could have magical powers without knowing it.
Base Breaker: Ashley. Some like her for being a good match for Elliot and a generally decent person, including towards her own seeming romantic rival. Others feel Dan is trying a little too hard to make her The Woobie.
Counterpart Comparison: There are a lot of similarities between Ellen and Fluttercruel from the Pony POV Series. Both of them began their lives as copies of a main character, both of them initially believed that this origin made them worthless and acted hostile, violent and suicidal as a result. To their surprise however, both of them were accepted by the people they were copied from, who viewed them not as merely clones but as a member of their family, and eventual became a valued member of the cast.
Chika won this status after five Q&A comics with her, even despite general "enough of Q&A" reaction on EGS forum. The Demonic Duck, who went from a convenient plot device to a minor character, may also qualify.
Lord Tedd even more so, in spite of being one of the most mysterious figures in the series.
Susan was originally intended by the author to be a minor secondary character, but she has taken on a life of her own and become part of the main cast. Also, while she wasn't exactly lacking in popularity before, developments that strongly hint at a future relationship between her and Elliot have caused her popularity to skyrocket.
Ashley has had very little screen time to date, even considering her status as a newer character. Despite this, her Genki Girl disposition, highly emotive face, and tendency to be the Plucky Comic Relief in already comedic situations has made her a fan favorite almost instantly.
One of the most popular pairings in the fandom is between Elliot and Justin, as evidenced during a sketchbook where Dan asked his fans to choose which two of his characters would be drawn kissing ... Elliot and Justin won by a landslide!
A lighter example occurs when Ellen laughs at the revelation that Elliot must release his magic buildup by turning into a girl, while she just has to shoot beams. Then she learns that she only has to do so a couple times each morning while Elliot has to transform every six hours and go to sleep transformed. She feels so guilty that Elliot has to encourage her to joke about it.
Panel 2 of this comic has Ed making a joke about son's tendency for transformation. Funny then, not so funny when the same scene is part of a montage showing his disapproval of Tedd's gender fluidity.
Furry Fandom: A segment of the fanbase and heavily played up in early arcs. Hasn't come up as much in later years as Shive grew out of the fandom.
Genius Bonus: In a filler comic, the Demonic Duck informs Dan that he's going to Australia to discover his roots. There is fossil evidence of a large, prehistoric bird that lived in Australia which has come to be known as the "DemonDuckof Doom".
Growing the Beard: The first few strips served as a mildly hilarious introduction to the characters with No Fourth Wall. The beard stated to grow during the Sister arc and finished by the end of the Painted Black arc or the end of Grace's Birthday Party depending on who you ask.
Harsher in Hindsight: This strip, which shows why Tedd is so reluctant to tell his father about his magic mark and possibly about being genderfluid, as well, makes a lot of Mr. Verres's comments about Tedd's penchant for turning himself into a girl considerably less funny.
Launcher of a Thousand Ships: Elliot, Elliot, ELLIOT. Fandom has shipped him with Justin and Tedd. In-Universe, now that his relationship with Sarah is over he has being Ship Teased with Susan, Diane and Ashley. And not to mention his Erotic Dreaming involving girls who're already in a relationship, like Grace, Nanase and even Catalina claiming to be his lover.
Les Yay: It's common enough that some fans have taken to calling it "OMG LESBIANS!" whenever it shows up as a means of criticizing its frequency. The problem most people have with it stems from the Double Standard in there being basically no Ho Yay aside from some vague shipping between Tedd and Elliot from time to time.
Magnificent Bastard: A strong case could be made for "Not-Tengu" being one of these. He succesfully executes multiple Batman and Xanatos Gambits during the course of his first appearance and even shows skill at Xanatos Speed Chess keeping his cool even when faced with setbacks and finding ways to turn those setbacks too his advantage.
Mary Sue: Grace most often gets accused of this as her adorable cuteness and prettiness and all around goodness is a constant thing in comics she appears in. She's so cute that she can get characters to do things they might not want to do by giving puppy dog eyes and anyone who's mean to her is seen as being irredeemably mean or evil. Her faults are things like clumsiness or naivete or hyperactivity that serve only to make her cuter and more lovable and she's one of the most powerful characters in the series. On top of it Dan has "jokingly" said before that hating Grace makes you evil. All of these have earned her the derisive of name of Gracie Sue among a segment of the fandom.
This comic lampshades Nanase's status as one as well.
Moe: Sarah, Rhoda, Grace, Catalina to a lesser extent, even Susancan be. On the (usually) male side, Tedd and Justin.
Nanase's hairstyle in Dawn of a New Era also evokes this, at least to Word of God.
Narm: The page where the mysterious entity that's been following the main cast and manipulating Magus reveals her name is meant to be a dark, climactic scene, but the gravity of the moment is somewhat spoiled by the fact that her self-appointed moniker sounds like it came straight out of My Immortal. For the record, it's Pandora Chaos Raven.
Chaos' manifestation on the physical plane will give you chills with her first appearance. When unfocused her image will haunt your nightmares forever. Which makes the revelation that she's the mother of a grumpy old history teacher all the more shocking.
And now she's returned, after being completely absent for several years of real time. And in the middle of what was thought to be a filler arc, too. Just her being there, not saying anything, just observing, is enough to send shivers down your spine.
"Family Tree" initially seems to be full of typical, if mind-altering, Gender Bender fun. Then Diana come back to grab a slice of pizza. Things quickly descend into horror fuel as we watch her slowly realize something's wrong. And by something wrong, we mean the terror in eyes as she tries to get her sister to remember that no, everyone is not a girl and please stop worshipping her and calling her "lord". Really, this is possibly the comic's darkest, most terrifying arc yet. The whole thing reads like a Lovecraftian Survival Horror. Then Tengushows up.
For extra horror Regardless of whatever gender the guests originally were, they're all gradually turning into clones of Nanase. Tengu is thorough in his attempt at identity murder.
Ship Sinking: Elliot and Justin are still a popular couple for the shippers, but as the comic progresses, there have been a number of things that the author has done to sink this ship, not limited to basically hammering that Elliot is straight with no gay leanings whatsoever, and having Justin seemingly get over his crush on Elliot off-screen.
Ship-to-Ship Combat: With the raising Ship Tease between Elliot and Susan, there have been mixed reactions. Elliot is the perfect candidate as Susan's potential love interest, since he literally "fails at perversion" and Susan's looking for a good man. But Elliot is already in a relationship with Sarah, Susan's best friend, so she's in risk to fall into a Yoko Oh No situation. In-universe, Sarah decides to break up with Elliot shortly before Elliot realizes she's like a sister to him, and she has no problem just handing him off to Susan (though she doesn't think it's likely).
Squick: The reason Damien wanted Grace so badly was so he could use her for breeding.
Never mind the Fridge Horror of the Family Tree arc. Punch spiking is one thing, but turning everyone into women, who are absolutely submissive and readily calling people their lord? That's pretty damn icky.
Since she was little, Susan has dyed her hair dark, so as to not resemble the woman her father had an affair with. These issues were vaguely addressed at the end of Grace's Birthday, but just as clearly shown to still be there in her mind. As of July 7, 2010, Susan's hair has permanently changed color for reasons unrelated to this, completely ignoring the reasons she did it in the first place.
Not completely unrelated. She dyed her hair because her natural hair color reminded her of her father's indiscretion, which fueled her mistrust of men, following with her love of using the Hammers to deal with obnoxious men. Her Awakening was triggered by the knowledge that the Hammers were created to promote obnoxious male behavior in the first place. With her Awakening, she no longer is Tiffany Pompoms pretending to be somebody else, she is Susan.
Also, Justin in general. His crush on Elliot and all thing involved were never really developed (unlike the MANY other issues from all other characters) and is pretty much forgotten by even Justin himself at some point when him being gay were old news and the crush served no propose anymore. His romantic life and development is non-existent, while everyone gets loads of it. His battle prowess, when put at test (it was awesome), is downplayed some chapters later by the Grace and Greg versus possessed!Dex and his fire golems battle. While Justin was hyped for throwing one golem into a river, Grace and Greg curbstomp them to the point they use said golems to teach Grace a sleeper hold in middle of the fight!. As another person pointed above, Double Standard may apply, since no potential romantic interest for Justin has been shown or developed... while we have a second, Catalina and Rhoda, which are newest characters that Justin, to boot, lesbian couple, on top of all the Les Yay in the comic. In fact, most, if not all, of Justin's romatic or Ship Tease scenes the kiss with male!Susan in Grace's birthday party, and timidwoman!Elliot blushing at Justin have either side as a girl. Did I mention that Justin is gay?.
Potentially rectified at the introduction of Luke, but it remains to be seen whether Justin will be given a larger chance to develop and fight back against threats.
Unfortunate Implications: When Elliot is thinking about morphing into a sexy form as a way of using his power for Self-Fanservice, there's a series of panels where each female form he considers fantasizing about explaining why he shouldn't ... ending with 'a random bikini model' saying, "I'm someone's daughter, you bastard." As opposed to, say, "I'm a person." Classy, Elliot — classy. (Though this is likely a parody of a very common shaming tactic to make somebody feel gross, rather than guilty, about fantasizing about somebody).
One Q & A comic discussing whether or not Elliot's disguise forms are bisexual pretty much labels them all by the worst stereotypes of female bisexuality: straight all along, narcissistic goths, and people pretending to be lesbians to snare guys and break the hearts of "real" lesbians. As if Shive didn't already have a bad track record...
A case can be made for this being a joke told from the point of view of a character that doesn't necessarily reflect the views of the author, though. Said character pretty much admits she's harboring animosity based on a bad experience.
As mentioned above, it looks like Justin can only have romantic scenes if his partner is a girl, or he himself is one.