Originally, Catalina's hairstyle was meant simply to be cat-like, and while Dan figured it would be somehow possible as a hairstyle in reality, he didn't quite know how it would work. A bit of fan art, however, helped with that.
According to Dan, this is why Carol wound up related to Sarah as part of a Retcon.
Dan suggests that Nanase's "magic boobs" are a result of magic affecting physiology after many people questioned how she could be so well-endowed despite her athleticism.
Fan Nickname: Several, mostly relating to bent gender forms.
Man Nanase is Manase, for instance.
Also an authorial nickname for Assistant Director Liefeld. Author's notes refer to him as "Muscle McMuscles".
Ellen's cat form has garnered the nickname "Katelyn".
Some parts of the fandom have named Grace, Gracie Sue.
Before his name was revealed, fans referred to Abraham as "Rocky."
Some fans who can't stand the name Cheerleadra tend to use "Mopergirl" as a super hero name for Elliot.
The arc villain of the Family Tree storyline is called not-Tengu by the fans due to the fact that Tengu was just his online handle and no one in-universe was interested in hearing what his real name was, cutting of all his attempts to give his name.
Ashley who has a crush on Elliot is given the nickname Ponytail Girl and variations thereof due to her distinctive side ponytail, and the fact that it took a while before readers learned her name.
Flip-Flop of God: Originally Dan was very against referring to the Aberrations as Vampires, since he envisioned them as have different origins and designs than most vampires, with the only similarities being that they were once human, they eat people, and they may have similar powers like hypnotism and immortality. He even had Susan go out of her way to refer to the first Aberration she met as a "not-vampire" and explain in detail she he wasn't a vampire even if he seemed similar to one. Eventually though, Dan realized he shot himself in the foot trying too hard to differentiate the Aberrations from Vampires to the point where that's all fans could associate them with, and decided in-canon that everyone just refers to them as Vampires even if they are still technically something completely different.
I Knew It: There is a section on the fan speculation page with confirmed or partially confirmed pages. Dan Shive has also mentioned in commentaries that he received messages from fans that correctly guessed certain plot points on several instances.
Jossed: Dan Shive, has done this too many times to count. In fact, the comic formerly seen on the trope page is a filler sketch made in response to a massive in flux of crazy and just plain wrong theories.
Schedule Slip: For a very long time, Dan was all over the place, barely squeezing out two strips a week. Grace's birthday party was one of the worst. He eventually started falling into "No set schedule, but frequent updates," but eventually started updating every weekday (sometimes skipping Wednesday if it's a bad week).
Shrug of God: Some things have been left ambiguous. In the case of Grace's ethnicity, Dan has said that he'll never make a direct clarification, one of the stated reasons being that fans have posted theories they're happy with and he'd rather not say if they're wrong.
Technology Marches On: At Grace's birthday party (written in 2005), Sarah brings a camera, and mentions that it has a 512 Mb memory card. While a memory card that size isn't completely obsolete yet, it's still quite a small card by today's standards.
After big storylines, Shive often does a few strips detailing the planning process. After Painted Black, he noted that originally it was going to be Vlad hunting Grace instead of Hedge, leaving a trail of corpses across the countryside. Considering that the arc is already one of the least favorite among the fandom due to Cerebus Syndrome, you can understand why he didn't want to make it even darker.
Dan frequently refers to what could have happened had he done the uniforms plot as a briefer standalone arc instead of a B-plot that ultimately lasted five years.
Word of God: Dan Shive keeps up a lot of running commentary, including behind the scenes decisions not directly reflected in the comic, with occasional comics devoted to Q&A. While he avoids the forum, apparently because of repetitive, predictable complaining when he was active there, he has been answering questions via formspring, although he seems to be very selective about which questions he answers. He tweets liberally about El Goonish Shive, often using the hashtag #EGS, and answered questions from the Ask Me Anything button on his / the comic's tumblr show up regularly in his posts.