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El Goonish Shive
This panel and the later design of Susan can make you think of this, perhaps?
In this panel, Tedd's avatar is wearing the girl's uniform from Azumanga Daioh.
Similarly, in the same strip Sarah is wearing the Gryffindor uniform.
And Tedd's little Imagine Spot about his keyboard bears remarkable resemblance to Zorak
Pandora Chaos Raven - Ebony Dark'ness Dementia Raven Way?
Angels Pose The photo session in "Lady Mysterious" mini-arc.
"OBJECTION!!!" Elliot's outfit here is a reference to this strip of .
The Wotch " Beats Getting Tackled by Some Stuffed Tiger Everyday at Least".
In the editorial for this EGS:NP comic Dan said it was meant as a homage to .
Plan 9 from Outer Space "I assure you that the extra with the hat in the last panel is certainly not intended to resemble anyone in particular whatsoever, though it is apparent that he is a man."
Grace is quite skilled at Super Smash Goons Melee.
In one strip, Ellen's mother tells her to wake up Elliot. She is " unspecific as to how".
In this strip, Grace declares Susan " Susan the Vampire Slayer".
The Complete Works of were used Frank Miller to help Susan learn hammer-summoning.
Shive admits that Susan's line here reminds him of the speech patterns of River Tam. Not to mention it's caused by a "serenity spell".
And in the strip before that, Susan's Awakening looks a little like she's turning into a reverse Super Saiyan, at least if you ask me.
So Immortals effectively die and are reborn in different bodies with different personalities? Sounds like a certain immortal doctor.
Speaking of which... Panel 3 of this comic. Take the glasses off that man, what do you get? That is the Eleventh Doctor, bowtie and all. According to Dan Shive, the resemblance was "amusing, but it wasn't something I planned". However, there's a good reason why that's probably not THE Doctor:
If defying the laws of physics made
cry, he'd never get anything done.
Nanase makes a shoutout to Mallrats here.
Tedd likes Mythbusters.
This one is made of shout outs. Batman, Green Lantern, Iron Man, Spider-man, two separate Star Wars movies ( The Phantom Menace and The Empire Strikes Back), and Captain Marvel. They're all in-universe shout outs on the part of one guy who works at a comics store.
The last panel of this one is a shout out to Dilbert. There's even a Pointy-Haired Boss.
Panel one is a subtle shout out to Clerks.
Apparently, Grace likes My Little Pony: Friendship Is Magic.
Justin claims that Noah ran off like a dog who saw a squirrel.
The Lucky Bunny Bounty Show seems to be a reference to several anime series and Firefly.
This strip is obviously inspired by The Legend of Zelda.
This strip parodies .
Man v. Food Sarah is apparently channeling the spirit of Elmyra (or the Looney Tunes Bigfoot Elmyra's dialogue was inspired by) in this strip.
Is that Ternaldo?
The title (not shown in the new website layout) of this comic is an obvious shout out to the main character of fellow gender-bending webcomic .
The Wotch It has been mentioned in-universe that the most obvious superhero name for Grace, Squirrel Girl, has already been taken by Marvel Comics.
Nanase kicked it up a notch. Bam!
Dex's mark that lets him summon fairies is shaped like Navi.
Q&A #5 references Conan O'Brien here, and the impractically pale-skinned elf here has a very familiar hairstyle.
In this filler strip, Dan's minion answers reader e-mails, and he comments "Just call me Strong Minion."
The magic nose beepage at the end of Painted Black is pretty similar to the divine nose beepage (at 7:35) from Dogma.
More likely it's a reference to where Lucy would often poke Snoopy's nose while saying "BEEEP!"
Peanuts Agents Wolf and Cranium are a subtle reference to Mulder and Scully from The X-Files. Aside from their job, and their appearance, the names "Wolf" and "Cranium" are possibly stealth puns on "Fox" and " Scully".
Also, Mr Verres has a poster on his wall that declares " The Truth Ain't Out There".
The Uryuom couple William and Gillian may be named after Fox's middle name and Scully's actress.
At an interview at Susan's video store, Elliot meets Mister Tensaided, who makes a blatant Matrix reference...which goes over Elliot's head completely.
Tensaided's opinion on Elliot.
Tensaided: I think he should be condemned. He has serious metal fatigue, his wiring is substandard, he's completely inadequate for our sales needs, and his brain is like a demilitarized zone.
Are...are you paraphrasing a
to describe a
How does that even—
Tensaided: At least you got the reference!
Apparently, Raven thinks about Burn Notice
8/16/12: Grumble Grumble
When Raven's in hospital, he's visited by " a lowly intern with a remarkable resemblence to Zach Braff" and a habit of tilting his head while he goes into his imagination. In the next strip, Pandora suggests that disguising herself as a doctor who modelled himself on a different medical show would have been " a lovely opportunity to hit that intern with a cane".
Strangely enough, Chaos, of all characters, seems to reference Mario in panel 4 of this strip.
" ...frankly, my commentary, I don't give a damn.
" " Say hello to my gauntlet! 
In this strip Ellen says, "Well. Maybe I DID get my peanut butter in your chocolate." as a reference to the early advertisements for Reese's.
Gav Bleuel teaches physics at Moperville South.
This has a reference to Mulan.
Girl:(Justin's) as mysterious as the dark side of the moon.
And a reference to certain comic characters and those who gotta slash 'em all:
Justin: And you're dating. I think I've read that fan fiction.
The internet is a wretched hive of scum and villainy.
This strip has Elliot's parents refer to " that video game bowling system".
Nanase and Ellen: Charlotte's Angels
When Tedd promises Sarah a reward for being his test subject, Sarah sarcastically asks whether it is cake.
Grace comes up with a unit of measurement for sadness called a Seymour, which uses the "Jurassic Bark" episode of as a baseline.