This is based on opinion. Please don't list it on a work's trope example list.
Tear Jerker / The Girl Who Leapt Through Time
Makoto breaking down in tears on the school roof when she believes that she's screwed everything up and can do nothing to fix it.
Makoto's final Time Leap.
And again, when Chiaki reappears for a few brief seconds after just leaving Makoto sobbing her heart out and tells her he'll be waiting for her in the future. Makoto's response is a bright, if extremely tearful smile and a quiet, "I'll come running."
For those watching the DVD, the included music video for the song "Garnet" can be this, especially if watching and listening while reading the subtitles.
I'll burn the days that I spent with you into my heart
So that I'll be all right even if I don't remember them
Even if I fall in love with someone else someday
You will always be precious and important to me
And this season will come around again
Makoto being unable to save Kousuke and Kaho, which lead to their deaths. Thankfully, Chiaki managed to fix it, but still....
The student who Makoto switched with in Home Ec. class. He's bullied relentlessly to the point he not only attacks his tormentors, but Makoto.
Chiaki. Dude leaped from devastated future where he doesn't even has a chance to see the sky. And partly thanks to Makoto, he ended up wasting his final time-leap charges before he could see the painting he came for in the first place...
Makoto's inevitable declaration to Yuri in the ending that she loves Chiaki. Even though it ended on good terms, Yuri's subtle expression afterwards is hard to watch. "Time waits for no one" indeed.