Shuichi Nitori and the Non-Conforming Community

With a calm atmosphere, down-to-earth characters, and a genuinely honest tone, Hourou Musuko (2013) attempts a relatively realistic take on transgender issues (as opposed to something like this).  The series explores, primarily, the life of the main character Shuichi Nitori, who is introduced as a boy with a feminine appearance and feminine tastes.

Over the course of the series, and with the significant support of several friends and role models who also struggle with LGBT+ issues, Shuichi comes to terms with her identity as a transgender girl.  I'll use female pronouns to reflect this.

Aoi Hyodo and the Test of Manhood

For a series that can spark a 'cross-the-board range of opinions on gender, feminism, and androgyny, one needs to look no further than Kaichou wa Maid-Sama! (2005).

Kaichou wa Maid-Sama! (literally, The Class President is a Maid!) is exactly what it says on the tin:  By day, the heroine Misaki is the tough-as-nails president of her school's student council, to whom all the male students must bow down.  But after school, she's a mild-mannered cosplaying waitress in a maid cafe, who must who cater to her male customers' every whim.

Obviously, a strict framework of gender identity is very potent in this series... while at the same time there are ventures by many different characters to cross those lines, the acceptable limits of which are constantly tested.  One of Misaki's classmates, Aoi Hyodo, embodies this test perfectly.

Yuri Kamanosuke and the Rejected Role

The anime Brave 10 (2012) is a historical fantasy that follows a journey to unite a group of ten ninja warriors who represent different elemental powers.  As the show touches upon themes of light and dark, good and evil, the character to be discussed is a highly sadistic and twisted hero who may challenge this binary... and, of course, challenges other binaries as well.

The warrior of the wind, Yuri Kamanosuke, is introduced in the third episode, using his own androgyny to his manipulative advantage.