This is based on opinion. Please don't list it on a work's trope example list.
Tearjerker / Superior Spider-Man
Ghost-Peter struggling to remember his name as his identity is wiped out. Seeing him broken like that so that Otto can remain Spider-Man was heartbreaking.
Ghost-Peter forgetting who Uncle Ben was in the process was particularly heart breaking.
The fallout from the "Run, Goblin, Run" arc. Norah Winters has lost her job because she was too close to Phil, Ben Urich has had his nephew arrested and must take time off work since the unmasking was too public for the Bugle, Phil has lost everything and has switched over to full time villainy under the Green Goblin. Given that at one point he tried to be a hero, it makes his fall even more tragic.
The fallout from the Spider-Man 2099 arc is bitter over all:
In the end, Peter himself laments that someone had to die so that he could live.
To put this in context, the man he's mourning was the same one who hijacked his body and spent the last couple months utterly destroying his (Peter's) life. And Peter still mourns him.
Before he was utterly broken by the events of "Goblin Nation", Otto was on the verge of proposing to Anna Maria. This makes his Heroic Suicide all the more tragic.
Otto's eventual fate. As arrogant and condescending and thoughtless as he was, all he wanted was to be a hero, to help people, to make the city a better place. He tries so, so hard to do the right thing, and in the end, he realized the dark side of "great responsibility"- sometimes you have to die so others can live.