If you're looking for manga similar to Wandering Son, you might like these titles. All recommendations are made by Anime-Planet users like you!
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.
This is a story about 2 childhood friends, Masato and Yuki, that reunite as teenagers. Masato is surprised to find that Yuki has become so cute, but even more surprised to realize that Yuki was, and still is, a guy. Yuki's affection for cross-dressing leaves Masato with feelings of discomfort and fright.