Blue's Clues has "you gotta have blue fur." The title character is of course, blue. There's also Green Puppy, Orange Kitten, Purple Kangaroo, Sprinkles (Blue's younger brother with a white coat and multi-colored polka dots) and Periwinkle, a cat.
Gaia's hair color at first was blackish blue (or downright black) with highlights, and took on lighter hues from season 4 onward.
Zarm, Gaia's Evil Counterpart, went the opposite way. At first, he had deep blue hair (with lighter streaks), which was later shifted to black.
Aelita from Code Lyoko has natural pink hair both in her Lyoko avatar and in the real world. She inherited it from her mother, who is shown in flashbacks to sport the same hair color. It stands out as the rest of the cast has a normal range of hair colors for French kids (assuming Odd's purple spot is permanently dyed).
Well, most of the rest of the cast. William's mother has green hair, as well as a DJ girl prospect in the episode "Crash Course". And Chris Moralès has white hair.
Odd's mother has mauve hair.
On Creative Galaxy, show star Arty is bald, but usually wears a blue cap that has his antenna and horn sticking out. Arty's friends, however, all have hair that is a darker version of their skin color - purple, blue and pink.
Danny Phantom from Danny Phantom has this going on. In human form, his hair is black, but when he "goes ghost", it turns white — and glows, apparently. And some of the ghosts have strange hair colors — Ember's hair is blue (and on fire), Kitty's is green, and Technus's is also white. Otherwise, it's a normal range.
Taken to an extreme with Doug, which not only has a rainbow of hair colors, but skin colors as well. Doug's best friend Patty is a Dark-Skinned Blond, and his other best friend Skeeter has blue skin.
Hi Hi Puffy AmiYumi has a particularly bizarre case, wherein one character has razor-cut blue hair and the other cottony pink hair (the latter also has anti-gravity pigtail-like spheres of hair above her head). The bizarre part is that the characters are supposed to represent two actual people, both of whomnote typically sport long, wavy black/brown hair.
Many characters on Invader Zim have oddly-colored hair.
Interestingly, every significant female character seems to have either blue or purple hair — Gaz, Tak in her human disguise, even Zita and Gretchen. The only exceptions are hairless aliens and characters too small to really care about.
Jem: One could argue most of the characters dye their hair since they're all rockstars, but a flashback to the main characters' childhoods reveals that, with the obvious exception of Jem (being a hologram and all), all the women had blue, purple, and pastel red hair even when they were kids. Clash was born with bright purple hair.
In KaBlam!, Henry has green hair, June has sky blue, and Loopy has robin's egg blue.
On Lady Lovely Locks, the eponymous character's eponymous locks are blonde with purple and pink highlights.
Lincoln Loud of The Loud House has white hair, while his sisters are either blonde or brunette (Lucy, who has black hair, dyes it and is naturally blond). Though Word of God said that it's not his natural color, several flashbacks and baby pictures show he's had it for most of his life, hinting it changed color during his baby years. It's not out of place for the family; however, as several characters comment that his grandfather had a similar case.
Buck from Mega Babies has dark blue hair to go with his blue skin. We also have Meg with Girlish Pigtails in green to contrast her pink skin.
Played straight, Lampshaded, and Averted in Pepper Ann. Pepper Ann dyes her hair green, in which her friends are indifferent about, causing Pepper Ann to call Milo out on having Blue hair, which he admits his hair is so naturally black it has a blue tint.
Most of the human characters in Phineas and Ferb have plausible hair colors, except for Ferb, who has green hair.
Also, most animals are colored somewhat like they are in real life, except platypi, which are all colored bluish-green.
Except the stuffed one in the museum at the end of the chariot race, which is brown.
On Pinky Dinky Doo, Pinky's hair is pink and her brother Tyler's is blue. In the original books, Pinky's hair was yellow and Tyler's was pink, until the book Think Pink.
Almost all of the Color Kids from Rainbow Brite have unusual hair colors. Rainbow Brite having normal hair is justified as she was originally a normal human girl named Wisp. Their horses aren't much better.
Ignoring the yellow skin, the characters of The Simpsons include some naturally blue-haired characters such as Marge, Milhouse's family, and the appropriately-named Blue-Haired Lawyer. There are even some purple-haired people such as Patti and Selma.
There are also characters with green hair (Krusty, Sideshow Mel) and maroon hair (Sideshow Bob).
Marge may have been naturally blue-haired in her younger years, but everyone knows that, these days, she dyes it with Blue #52 (or is it Blue #56?). Also subverted with Patti and Selma. Their true hair colors were hidden under smoke and ash.
Chief Wiggum also has blue hair, but it was black in early episodes. Also blue-haired are the "Blue-haired Lawyer" and Waylon Smithers, when he was an African-American in the episode "Homer's Odyssey".
As Soar Loser in Skysurfer Strike Force, Brad Wright dawns a lime green wig. Bioborg, Dr. Five Eyes also has lime green hair.
Mayor McDaniels from South Park has turquoise hair, while Nurse Gollum had pink hair. While most characters' hair is colored within the plausible range, there were occasions where background characters would sometimes be given bright blue or purple hair.
Steven Universe features this, but generally limits it to the Gems. Rose Quartz had pink hair, Amethyst has a pale lilac mane.
Jasper's is snow white (tinted orange in some lighting), Peridot has light green hair and Lapis has blue hair.
When Garnet was first born, she had pink and blue hair, rather than black.
One episode featured a punk-rock girl who beared some resemblance to Rose, and thus catching Pearl's eye. Pearl asks Steven if humans "come with pink hair," to which Steven informs her that it must be dyed.
On Strawberry Shortcake's Berry Bitty Adventures, only Orange Blossom and Huckleberry Pie have realistic hair colors (dark brown and medium brown respectively). Strawberry gives "redhead" a whole new meaning, and despite Lemon's blonde moments, her hair is definitively yellow. Cherry's hair is a deep purple and occasionally sparkles. Blueberry, Plum, and Raspberry's hair colors can't be found anywhere outside a bottle in the real world.
In Team Umizoomi, We have Geo and the Blue Mermaid, who both have blue hair.
Teen Titans has the green-haired (and skinned) Beast Boy and the violet-haired Raven as part of the main cast (Raven is explained as being part demon). In season 5, we're introduced to Kole, who has bright pink hairnote Although an animation error in "Titans Together" would depict her with orange hair, which she had in her early concept art and in the original comics. Jinx is a villain example, with her hair also being pink.
Frida of El Tigre has bright blue hair. So does her father and her unseen grandmother, implying that it is genetic. That, or certain members of the Suarez family must dye their hair blue.
Amanda Duff, Elmyra's older sister who appears in the Tiny Toon Adventures episodes, "Take Elmyra Please" and "Grandma's Dead" has purple hair. Given the fact that her father, MacArthur has brown hair and her mother, Emily has red hair, it's possible Amanda dyed her hair purple.
In Total Drama World Tour, Sierra has completely violet hair, it's unknown whether it's "real" or dyed. Gwen and Duncan also have teal and green respectively, but it's dyed.
Max also has purple hair (and oddly grayish skin), again with no real explanation.
In Trollz, most of the characters have oddly-colored hair. Amethyst has pink, Sapphire has blue, Onyx has purple, Coal has green...Oddly enough, Ruby's hair, fire-engine red, is stated once to be dyed. Her natural color is brown.
Mara in TRON: Uprising has light blue hair; this is notable because almost every other program in the Grid has black, dark brown, or grey hair.