The mini comic "Leah". What makes it even more of a tear jerker is that the writer made it in remembrance of a friend.
"The Kid Who Collects Spider-Man," in which Spider-Man visits Tim, a nine year old fan. The story's heartwarming enough already (especially when Spidey shows Tim his secret identity), but what really gets readers is the revelation at the end that Tim was diagnosed with cancer and given a few weeks to live.
"Maybe Next Year" is an issue about Peter remembering his Uncle Ben's tradition of taking him out to a baseball game. They support a team that (almost) never wins, but they have to keep cheering...
The water works increase by the end. The last game he went to with Ben reveals that for once the their team actually wins, which causes an excited Peter to finally understand Ben's message of always supporting the team no matter what... And then after this heartwarming moment the narration reveals that this all takes place just three days before Ben's murder.
One More Day, the comic that pissed EVERYONE off ends on a depressing note. When Peter and Mary Jane are about to lose their memories, Mary Jane says this:
"Peter, whatever he [Mephisto] does or undoes, it doesn't matter. Because whatever he does to pull us apart would have to be stronger and bigger than what brought us together and kept us together, no matter what happened. And there is no power in the universe big enough for a job like that. Not the devil, not god, not ANYONE. We will find each other and be together again."
In ASM #700, Peter dying in Doc Ock's body.
Oh, it gets worse - no-one, not Peter's friends & family or the rest of the Avengers, knows the switch happened. Aunt May & Mary Jane watched Peter die & didn't realise it.
You think that's bad? In issue 9 of Superior Spider-Man, Otto erases Ghost-Peter and all his memories after a No-Holds-Barred Beatdown and (arguably true) "The Reason You Suck" Speech. Peter is destroyed after losing all his memories: of Uncle Ben, of Captain Stacy, he even forgets HIS OWN NAME.
In Spectacular #200, Harry in Green Goblin gear abducts MJ and takes her to the bridge for a little talk. MJ accuses Harry of wanting to push her off like Norman did to Gwen. Harry takes offense and reveals how much Gwen's death has affected him.
"You know... I still miss Gwen. So much. There are times... even after all these years... when I just can't believe it. 'It can't be true,' I think. 'She can't really be dead.'"
The last two pages of the story, where dialogue-less panels depict Harry dying and Spidey breaking the news.
As Harry is dying after snapping out of the Goblin persona and saving Peter, Peter asks him why he did it, and Harry gasps out his last words: "How could I not, Pete? You're my best friend." And much like Aunt May's death, the company saw fit to taint this moment, only this one with one nasty Thanatos Gambit.
Yes it's part of The Clone Saga but that doesn't stop the 3-issue miniseries Spider-Man: The Lost Years from being this. Kaine gets it the worst though when his clone degeneration accelerates at the same time he finds out Louise Kennedy, the woman he'd fallen in love with, was really a Dirty Cop which is enough to make him snap.
"Even then I wanted to call out to her... beg her not to leave me. But I'd humiliated myself enough. Even Professor Warren hadn't made me feel so small, so... ridiculous. Then why did I cling to these feelings; exult in them? Why did I drink from my cup of shame slowly... relishing each small sip? Perhaps because the source of my shame was her. The only love I'd ever known. The only love I ever would know. And I wanted to savor even the dregs of that love... before I destroyed her."
If you can get past the whole Mary Jane dying because of radioactive cells from having sex with Peter, then the story can actually be quite sad, like when Doctor Octopus gives the original Spider-Man costume back to a crushed Peter Parker, but Doctor Octopus was already dead, trying to find Peter so that he could bring the age of Super Heroes back, he put a recorded message into his arms to deliver this.
What happens to Sandman's daughter. He wasn't even aware of her existence, and he only realizes her true identity right before she's murdered by the Mayor's thugs. His horror and grief at her fate is what ultimately gives him the strength to rebel and help Spider-Man defeat Venom and rid New York of its fascist regime.
Even his debut ends with one. You know? Uncle Ben's death?
Peter: My fault... All my fault... Because I didn't stop that punk when I could have! Now Uncle Ben is dead! He's dead!!!
Amazing Spider-Man 657, particularly the last page, always has this troper in tears. This was right after Johnny Storm's death and Peter's going to mourn with the Fantastic Four. The whole comic alternates between being a tearjerker and a Crowning Moment of Funny, but it ends on a particularly tearjerking note with Peter watching Johnny Storm's video-will of sorts, in which Johnny not only gives Peter his spot on the team, but his spot in the Fantastic Four family.
Johnny: If youíre hearing this, Iím sorry, pal. Sorry that Iím gone. ĎCause... well... I know how you feel when it comes to losing family. And thatís what you are to me. Family. So... if youíre thinking of this as my last will and all... Iím not leaving you my sports cars or stuff like that... Iím leaving you the best thing I ever had... My spot on this team. A place in this family. The best sister, two brothers, niece, and nephew a guy could ask for. They— We all love you, Pete. So? You up for it, bro? Weíre all here for you.
"The Final Curtain" from Spectacular Spider-Man #27. It starts with Peter visiting Uncle Ben's grave on Christmas Day to have a chat with his ghost and wish him Happy Holidays, and it slowly slips into Peter sharing a recurring nightmare about finally being defeated by his foes, all interspersed with flashbacks of a seven year-old Peter freezing up on stage during a class play. Peter comes clean about all of the crushing fears and insecurities that he deals with every day when facing his Rogues' Gallery... and it gets all the more heartbreaking when Uncle Ben pointedly tells him, at one point, that he's not really there, and that Peter's just talking to himself. In the end, there's no one with whom Peter can be this honest about how much being Spider-Man scares him, but he still puts up with it every day, because, well... it's his responsibility.
During the Gauntlet, Peter Parker was unemployed, cosmically divorced, and being battered by his classic enemies. The only good thing to come out of everything was that Aleksei Sytsevich, the Rhino, had married and reformed. When the new Rhino kills Aleksei's wife, Spider-Man desperately pleads and struggles in vain to keep Aleksei from becoming the Rhino again and is left with nothing but fear and loneliness when he fails.
A sound comes out of Spider-Man that's so soft it screams. It's the sound of his heart breaking.
The Gauntlet seems to be full of this. Another case of Tear Jerker, mixed with horror for good measure appears when Curt Connor loses control of his Super-Powered Evil Side and kills his son Billy. It's horrifying and heartbreaking because it depicts a father losing control of himself and killing his own child. Even worse, the experience essentially destroys "Curt" as well, leaving the Lizard in charge.
They piled it on stupidly thick in The Gauntlet. Little Keemia screams at Spider-Man that she hates him. He'd gotten involved in a murder case when a friend of his was implicated for screwing up the evidence, to find that the victims, a woman and her lawyer, were involved in an acrimonious fight with Flint Marko, the Sandman. She'd been snowing him into believing he had a daughter, even though it was no longer physically possible for him to have a child, and he'd become so obsessed with trying to be a good father that a part of himself had split off and killed them in order to get them out of the way without him even being aware of it. Spider-Man defeats him and gets the girl back, but because her grandmother (who had been her caretaker when Marko took her) admitted she wasn't watching the child when she was taken, CPS is putting her in the foster system, after Spider-Man had promised her she'd be with her family in order to make her go with him. Not knowing what happened to her mother, Keemia had thought her "father" was a good father, and so having lost everything as a result of leaving him, views Spider-Man as a liar and a thief.
Aunt May: Well, you start by doing the hardest thing: You forgive yourself. I believe in you, Peter. You're a good person. And I know you'll find a way to put it right.
Uncle Ben's death, definitely. Peter arrives to find his uncle lying on the sidewalk. Peter calls his name and Uncle Ben hears him. "Peter...?" Peter says "I'm here, Uncle Ben." but Ben is fading quick and can't even tell he's there. With one last, desperate call out to Pete, he dies, leaving Peter to sob over his body. It's that last "...Peter...!" that always gets this troper.
The Parting Words Regret makes it even worse. Ben tried to impart a lesson, but Peter is too frustrated to listen. The look on Ben's face after Peter says his line is devastating.
Ben: I don't mean to preach, and I know I'm not your father. Peter: Then stop pretending to be!
It's even sadder when you consider what really happened in Spider-Man 3. Because Peter let the thief get away with the money, he caused Flint Marco to accidentally shoot Ben. Really, that adds more guilt to Peter's conscious, inadvertently making him responsible for his uncle's death.
The ending. Peter finally has what he's always wanted, the chance to be together with Mary Jane... and he has to reject her to keep her safe.