A list of web comics in which characters have unusual hair colors.
Zoe from Sluggy Freelance is shown as having blue hair. Since no mention has been made of her mother berating her for dying her hair, we must assume that's her natural color. (Though, in an Alternate Universe, she has purple hair.) This is possibly the result of Pete Abrams's computer monitor not being properly calibrated during the early days of the strip; the same problem also caused Zoe's skin tone to be lighter than intended, forcing Pete to scrap his plans for making her half-Cuban.
Zoe is more a case of Hair Color Dissonance: her hair is black but is shown as blue-black, like Superman. Her mother has this too. However, the cannibal "Freaky" Fred has obviously green hair and this is never explained.
Sapphire and any other zombie character from Monsterful have different shades of blue, it seems that most (if not all) zombies have blue hair.
In The Dreamcatchers Masquerade, bright hair colors appear to be the norm as it takes place in a fantasy world and this appears on many of the main characters.
While most of the Girl Genius characters have perfectly normal hair colors, one character, Zeetha, has green hair. This is remarked upon, used as a plot point twice so far, and presumably is less weird in the Lost Kingdom she comes from.
Sanaa Wilhelm has pink hair.
Although her brother Othar Tryggvassen does make a comment to the effect of "What have you done to your hair?!", implying that hers at least may be a dye job.
There is Tarvek, with bright red hair, and his cousin, Violetta, with a similar, but darker color.
The Jägers' hair ranges from green to purple. Justified because the transformation also gives them weird skin colors and random non-human traits like tusks and horns, for that matter.
Tower of God: The blue-haired Koon clan and Yuri's pink-haired companion, codename Mrs. Strawberry Ice.
Plenty of this in Yosh! - almost all the robot girls, who can have any colour hair, and eyes and ears to match (but then they are robots), the Magi get hair colour coded to their power - blue for Water, purple for Power, red for Fire - which is confirmed as a side effect of their power - and then also Kate (Purple hair) and Blue (A clue in her name).
Ronin Galaxy: Giancarlo, and Leona, although the latter is blonde with blue highlights.
While Joyride has aliens and such, the only improbable hair color (from a human perspective) is the one human we see, as Rei has purple hair. Rafeal and Micheal have auburn hair.
In El Goonish Shive, Tedd has purple hair, his father has blue hair, and his mother has bright red hair despite being Asian.
Susan is naturally blonde, but dyes her hair dark blue. Several characters were surprised to learn that blue wasn't her natural color. Now it is, though.
There have also been various background characters with green, blue, or purple hair. Dan stated that all hair colors except Susan's are natural. This is brought up in one of the Q&A sessions. Upon reading a question asking whether strange hair colors are natural in the EGS universe, Chika wonders if the person writing it lives in a universe without brown, black, or blonde hair before giving a somewhat hesitant "yes". According to hisTwitter account, by the time Dan learned how to paint Tedd's hair without ending up with an ink blob, colors were already established and he liked the idea of this being a natural color, especially since EGS has visible roots in Anime.
Mostly subverted with most of the cast of Frivolesque, who all have relatively normal hair color. Played straight with Gaia, who has bright green hair, but lampshaded by the fact people in-universe do take notice of it. Saki also has dark blue hair, but the only one to mention it is Gaia.
In Fuse, many minor characters are given blue hair. This accidentally resulted in a page where there's more people with blue hair than not.
Antimony and her mother have red hair, bordering on magenta. It's so vivid that it earns them nicknames like "carrot top" and "Fire Head Girl".
Marcia Sutton has green hair. This, along with the fact that trees are Serious Business for her, is explained by the fact that she is a actually dryad, revealed shortly after her introduction.
In retrospect, these unusual hair colors all follow one consistent rule: everyone with an impossible hair color has some sort of non-human ancestry. Yes, that includes Antimony.
In The Order of the Stick, blue hair (both light and dark) is common in characters from the Japan-inspired and aptly named Azure City. Purple or teal hair is also possible.
This seems to be common with elves. Vaarsuvius has purple hair, Inkyrius has light green hair, their children have teal and orange hair respectively, and Aarindarius has pink hair. Team Peregrine also counts, with a pink-haired cleric and a white-haired wizard.
Celia has white hair, but maybe justified because she's an air elemental.
Fairly early in the strip, but spoiler tagged just in case: Gav is perfectly cloned, including his hair and memories, 950 million times, making blue the single most common hair colour in the galaxy in the space of a second.
In The Law of Purple, blue hair, along with black, brown, blond, and red hair, is a natural hair color for humans. Any other strange color means either that it's a dye job or that the person isn't human.
In The Dragon Doctors, Sarin the wizard has green hair and Kili's hair is bleach-white. This is explained as extraordinary circumstances, though, both resulting from different experiences they had with magic.
The common humans (and the Seraphim and Goddesses) all have this in Fetch Quest: Saga of the Twelve Artifacts. So far, only Nephilim Lachesis had dyed her hair, and it was all because she didn't want to look too much like her less refined twin sister Saffron. However, the Tangashen completely avert this.
In Aetheria Epics, normal hair colors for people in Veil include pink, purple, and green. Having black hair can give you away as an outsider.
Last Res0rt has plenty of justification for odd hair colors (what with all those aliens), but White Noise's hair has actually aged into a pale blue. His original hair color appears to've been dark grey with blonde streaks in it. (or was it blonde with dark grey streaks?)
Karcharoth of Cry Havoc has purple hair. Its unknown if this is natural, dyed, or the side effect of something he has done/been exposed to
Mitadake Saga (like the game it's based on) runs off of this trope. Each of the characters has an alias which is usually based on their often implausible hair colour. Bonus point for two characters with blue hair
In Antihero for Hire, Shadehawk has purple hair. It seems to be natural because it's still completely purple in situations where he couldn't obtain hair dye for long periods of time, and he once briefly had a purple beard. Several side characters also have blue or green hair.
Angora from The Meek has green hair in world of otherwise normal hair colour, and people definitely think it's unusual. It's justified in that it isn't her natural hair colour, but it looks green because moss grows in it due to her odd powers. It even sprouts little flowers! Flashbacks show her natural color to be a dirty blond.
In Olympic Dames, one of the main characters, Caitlyn, has white hair. It has yet to be explained, but flashbacks show it wasn't always white.
In Catena, the characters are anthropomorphic cats who also have hair as well as their fur. Most of them have the usual hair colors (blonde, brown, etc.) However, Bear and Bryony have pale blue hair, while Belle and Annie both have hair of different shades of pink.
The main character of Seekers has jade green hair.
Eddy of Gender Swapped has light blue hair, and his dad, Jim, has natural dark blue hair. Most likely influenced by the comic's anime based writing style.
Her daughter, on the other hand, is a more "conventional" Fiery Redhead.
In Wright as Rayne, Sarabeth, John, and Power have blue, very red, and pink hair respectively. Sarabeth's is confirmed to be dyed, though, while John's seems to be natural, judging by his also red eyes.
Liz from Blip has blue hair. Then again, she's a vampire.
Though the comic is black and white, Baalah from Pawn is depicted with blue hair in official artworks.
Dark elves in What Do You Do tend to have dark blue hair. Megan and Nathan being the exceptions with light blue and orange hair respectively.
In Questionable Content, a recent development has an AnthroPC named Momo transferred into a humanoid body with bright pink hair. Though one comic showed it changing color when someone pressed the bellybutton.
Myari and Elon of Ears for Elves have green hair. The former's hair is nearly neon green.
Several non-human characters in Charby the Vampirate have a veritable rainbow of colors, though most of the main cast has black hair.
And there are even a few characters with natural hair colors that change (usually to blue) when they transform into a Super Mode
Elijah And Azuu has love interest Fraja and her family, most of whom sport natural neon pink hair.
Ophelia in Star Something. The cast page describes this as "Species: Human with Purple Hair for Some Reason".
In Angels 2200, Loser has bright pink hair and Sprout's is neon-green.
Accel in Amya has bright blue hair, in keeping with his magic of choice being electricity.
In Band Vs Band, blue and pink are naturally occurring hair colors.
Kell of Kevin & Kell has blue hair, no explanation. In one early (black-and-white) arc she had to wear a wig but flashbacks to her childhood show her with the same hair color. Her identical cousin Sheila also has blue hair but slightly darker.
In Get Medieval, a linguistics professor has semi-natural pink hair due to relaxed genetics laws on her home planet. When she lands in feudal Japan, her crescent-moon shaped spaceship causes her to be mistaken for a divine moon princess. Then several hundred years later, Sailor Moon is created.
Sailor Moon Artist: I don't know, it just...makes sense for a moon princess to have pink hair!
Fiona Dae in Supernormal Step has blue hair. It's dyed, she's naturally blonde. For much of the comic it's coloured permanently with magic, although it reverts to blonde at one point when she uses up her reserves of power.
Interestingly averted with Homestuck, at least until TricksterMode, which gives Jane, Jake, Roxy, and Dirk pink, lime green, cotton candy blue, and Fanta orange hair respectively.