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Tear Jerker: Wandering Son
The general concept of the series can be this. Transsexual children growing up.. Anyone who knows about Transsexuality and that age knows how horrible that time is, especially since most can't transition and the body changes.
When we find out that Anna broke up with Shu due to her "crossdressing". It comes off as a sadly realistic problem, and a Tear Jerker since they were so nice together.
And the Tear Jerker goes away when several dozen chapters later we see they've gotten back together and Anna doesn't seem to mind Shu's transgenderism
Nitori notices her voice is changing, when a girl tells her that. The look on her face, and the dull surprise, really throws you off. The anime went for a different response, with Nitori smiling and seeming to come to terms with the change; which has a number of Unfortunate Implications.
When Nitori gets in trouble, and becomes the laughing stock of the school, because she wore a Sailor Fuku to school even though she isn't out as female. Takatsuki got off scott-free, but when Nitori does it she gets sent straight to the Nurses Office. This incident also makes Takatsuki stop wearing the boy's uniform.
After having such a nice friendship, seeing Takatsuki's and Chiba's bond break down can be a Tear Jerker. They eventually rekindle though, but it took around three years in-series.
On a similar note, seeing Chiba's dramatic change in personality through the early volumes. She became dramatically more stubborn, aggressive, and depressive.
This happens a lot to Nitori lately. Her haircut looking too masculine, going to the all-boys school, having to wear the male's waiter outfit at her new job..