Shuichi Nitori is an elementary school boy with a secret: he wishes he were a girl and likes wearing their clothes. With the right outfit and his cute, effeminate looks, he is often able to convince people that he is someone else - or even something else. Unfortunately, although his best friend and object of affection, Takatsuki, accepts him as he is, she does not return Shuichi’s feelings. Moreover, school is an unforgiving place and Shuichi walks a fine line between liberating his true self and being labeled a freak by all his peers...
Both series have major similarities due to their basis on questioning what defines gender. The two titles revolve around young boys (and in Hourou Musuko, a young girl) as they find that they don't feel correct in their own skin, don't feel like they're supposed to be boys and the series documents the journies these characters embark upon in hopes of finding acceptance and happiness.
Both manga are about schoolchildren that are crossdressing and, in some cases, suffering from gender dysphoria. Both treat the subjects with more respect than is usual in media (at least in my experience). There's much focus on the character's psyches, how they interact with each other and why they choose to present as the sex they are not assigned with.
Both manga are very similar in their subject matter and how they approach it, though they clearly differ in scope. They both feature a young boy struggling struggling and trying to come to terms with gender identity issues and it's presented in a touching and nuanced manner, and free from the fetishized aspects that are rahter common in stories such as these. Fans of either work shoud check out the other.
On the way home from work, male-to-female transsexual Maho meets Fujiko, the estranged daughter of a well-to-do family. After realizing they live in the same apartment and both work night shifts, the pair soon becomes inseparable, due to their mutual jaded personalities and detachment from normal society. Between drinking tea and gardening, the two women discuss gender and the frames that society imposes on people.
Double House and Wandering Son are both low-key, character-focused manga about gender etc. Tone and such are pretty similar, and there's not many manga that cover this topic without comedy or "traps", so if you're interested in one's themes you may as well check out the other.
Punpun is a relatively normal elementary school student; he goes to lessons, does his homework and gets on well with his classmates. Unfortunately, it’s everyone else around him that’s bonkers! With a crowd of crazy teachers playing hide and seek or having extreme reactions to even the tiniest situation at school, his father kept at bay on domestic violence charges, and only his unemployed layabout uncle to look up to Punpun’s life is anything but simple. However, despite the mayhem surrounding him, Punpun still continues to quietly live on, contemplating his dreams, experiencing the joy and terror of falling in love, and trying to deal with his anxieties about sex, religion, and growing up.
Both manga are about children growing into teenagers while dealing with issues like love, the onset of puberty, friendship and feeling disenfranchised or not being accepted for who you are. They're also very similar in that they feature a lot of characters, plotlines and angst. All this is told with an understated social-realist tone: there's not much in the way of melodrama or easy answers in either work.
I wholeheartedly encourage fans of either of these works to check out the other.
Another sensitive slice-of-life series about middle schoolers who feel different from everyone around them. Wandering Son deals with trans* characters, and Translucent is about a girl with the invented 'Translucent Syndrome', which makes parts of her body (and sometimes the entire thing) go completely invisible. Both tackle issues of acceptance, feeling uncomfortable in your own body, self-esteem, and just general problems that middle school students have to deal with.
Additionally, the main characters of both have an adult role model of sorts that has already dealt with similar issues (Translucent has Keiko, who's turned completely and permanently translucent, and Wandering Son has the fully-transitioned Yuki).
The tone, pacing, and general sentiments of both series are extremely similar, so if you enjoyed one, definitely look into the other.