Ascended Fanon: The apparent reason that Shinae and Gailen are a couple after the timeskip, since that was part of that year's winning contest entry. Also applies to the previous year's story, where Mikilu living with Taio'shi also seems to have become canon.
The trifecta of Snadhya'rune, Sarv'swati and Zala'ess Vel'Sharen is also referred to as "The Gorgon Sisters" by some. The Traitor Sisters is also pretty common.
An incident in Chapter 15 (Ariel being kidnapped by Rik and having to fight him off, only to have him die) has also been referred to as being "Rik-rolled" by several forum members. The authors were seemingly aware of this too, since the chibi comic at the end of that chapter where Rick's reason or kidnapping Ariel was so they can form their own band. The band is called Rick-and-Roll, and their first song even includes the line "Never gonna give you up".
Syphile gained the nickname "Sniffle" or "Sniffile" from both fans and detractors due to to the number of scenes where she utters some variation of the line "it's not fair". "SyFAIL" also seems to have become popular during the new Chapter 1, and even her distinctive high-collared cloak has gained a nickname, with some calling it the Failcloak since she seems to do something stupid nearly every time she appears in it, including right before she dies.
One of Sil'lice's daughters has been nicknamed some variation of "Pissin'hermouth" after her declaration in chapter 17 that she'll "Pin [Zala'ess] to a freaking wall and piss in her mouth". Her actual name is Kadara, but Pissin'hermouth has stuck.
Sha'sana quickly gained the nickname "Sasha" all the way back in the Prologue, and when she appeared in Chapter 25 it resurfaced again.
"Team Purple" for the extended family of Mel'arnach, Snadhya'rune, Kalki, Zhor and Ariel due to them all having the same hair (or in Zhor's case, fur) color. There was one Daydream wallpaper of them all together that spawned this nickname.
Naal's pet spider, usually seen on her back, is affectionately nicknamed "Fuzz Fuzz" by fans, not to be confused with Fuzzy, and was referred to by that name in one chibi page. Ironically enough, Fuzz Fuzz and Fuzzy now appear to have met similar fates. It's also referred to as "Naal's baby" due to a scene in the main story where Kiel tells a woman with a pack lizard that it's Naal's big ugly baby when she objects to having a spider in her cart.
One Illhar'dro girl named Layani who appears in Chapter 33 (second from the right on this page) was quickly dubbed Hammer Pants by the fans, due to her pants reminding people of MC Hammer's. Fans also noticed that she's sporting one glove like Michael Jackson.
And Crossbow Lady, an unnamedBadass Bystander in Chapter 38 whose response to Maki was a crossbow bolt in the shoulder and telling them to get the f out of their district.
Quian Jie'yen, the Jie'yen ambassador, was compared to a "Drow Heidi Klum" because of her extremely long legs.
What Could Have Been: Concept art from an unused sidestory that eventually became the "Syphile's Great Deed" contest story depicts Syphile's eyes as blue before becoming tainted. There's also a piece done by the official artist that shows her with purple eyes, but that probably isn't canon at this point.
There was also going to be a story at one point clarifying what happened to Laele, but it was abandoned for unknown reasons.