Personally, I love spotting characters in fiction that flip huge birds to the gender binary so forcefully imposed upon us all by the heteronormative patriarchy. It's a little sad that many of these characters are alone; a single token surrounded by a cisgender, binary cast, but they are delightful additions to many anime and manga that deserve more love from fans of the works they appear in. While such minor representation certainly isn't enough and honestly, isn't very realistic at all (since when do genderqueer folk go out of their way to surround themselves exclusively with The Cis Hets™?), it's still a small step in the right direction. In no particular order, here are some gender nonconforming and genderqueer characters in anime and manga that deserve more time in the limelight!
1. Aoi Hyoudou - "Maid Sama!"
Despite generally identifying as a cisgender male, Aoi poses as a woman on the internet due to his love of cute beautiful things. Over the course of the show, he comes to terms with being OK with being a guy who loves cute stuff!
2. Inugami - "Gugure! Kokkuri-san"
Though technically not human (Inugami is the vengeful spirit of a dog), Inugami is portrayed as able to present themselves as male or female without any particular preference for one or the other.
3. Nathan Seymour - "Tiger & Bunny"
What's this? A confident canonically agender queer POC? In my anime? With a relatable backstory? Who is capable of exercising greater control over his flame powers than most of the rest of the cast with their own powers? Who is a successful owner of their own company? Incredible.
4. Seiko Kotobuki - "Lovely★Complex"
5. Kuranosuke Koibuchi - "Princess Jellyfish"
6. Yuu Kashima - "Gekkan Shoujo Nozaki-kun"
She is beauty, she is grace, she is the handsome Prince Charming! Yuu openly flirts with her female fans and plays the princely roles in the Drama Club's shows because no guy in the school is better at making everyone swoon than her!
7. Pretty Much Everyone - "Otomen"
8. Masumi Okuyama - "Nodame Cantabile"
Behold Masumi, the gay timpani player that, when given free reign to pick a costume for the school festival, makes his own dress from scratch! This young man is a gift.
9. Isabella Yamamoto - "Paradise Kiss"
What's this? Is your thirst for beautiful trans ladies not satiated? Good! Have this goddess of womanly fashion, the mom friend, a blessing!
10. Hange Zoë - "Attack On Titan"
11. Crona - "Soul Eater"
12. Haruhi & Ryoji (Ranka) Fujioka - "Ouran High School Host Club"
13. Grell Sutcliff - "Black Butler"
More trans women! More trans women! More trans women!
14. Half The Cast - "Hourou Musuko"
Saving the best for last! This bittersweet story is about some kids in middle school coming to terms with gender dysphoria and identities. It handles their questions in a careful manner and addresses many struggles kids face when realizing that they may not be cisgender. The manga covers more than the anime does, but if you'd like a cute short story with a unique art style and good music, check out the anime.