Ultimate Spider-Man gets a few, but one of the most poignant is after J. Jonah Jameson fires Peter. After a run-in with the Kingpin's goons (during which Spider-Man saved him) and a fierce phone call from Aunt May, Jameson walks to Peter's house late at night and waits for him to return. He sits with Peter on the stoop and gives a heartfelt explanation of why he snapped and fired Peter when he asked what was so wrong with Spider-Man. Jameson, in a rare sympathetic moment, tells Peter that a few years ago his son, who meant the world to him, was killed in a NASA shuttle accident. The agency sealed everything off as classified, and Jameson didn't even get a body to bury. He says that his son was a hero, that men like that are real heroes, and that people like Spider-man just cause chaos. Even though the reader (and obviously Peter) disagree with him on that issue, it is such a heartwarming yet simultaneously heart-wrenching moment of weakness and grief from the grouchy old man that no one can hold it against him, topped off by Jameson rehiring Peter and telling him that he'll assign him to Ben Urich so that he can learn what reporting is really about.
And Jameson's realization that he was wrong about Spider-Man, something that sadly could never happen in the mainstream series thanks to Status Quo Is God.
The Venom arc, which deals with the fate of Richard and Mary Parker, has more than a few. It begins with Peter finding an old home movie of when his parents were alive, at a meeting he's actually forgotten. Every now and then we cut from the video to Peter just staring in shock at the screen. After a few pages, May comes into the room as well. Ben's in the video as well.
Richard's videos. Just seeing the man crowing about trying to cure cancer, and make the world a better place, compared to his later tapes, where he's just broken. And the reason for why he's trying to cure cancer: His father died of cancer when he was younger, and he doesn't want any other children to lose their parents. And what does he get for his troubles? Lawsuit after lawsuit after lawsuit, and we're never even given a reason as to why the company he worked for did this to him.
The Symbiote Wars arc makes it even worse, when Peter tries researching his father, and he doesn't find a thing. Not even a footnote. This despite the fact that he had published papers, he had done things in his life, people knew him, and now he's just an Unperson. Then, just to make things even worse, the company that did this to him appropriated his research and claim it's theirs.
The death of Gwen Stacy. It's just so quick and random. And meanwhile Peter is having one of the best days of his life since he became Spider-Man, until he comes home.
Aunt May tries to contact Gwen's mother afterwards. The woman doesn't care to listen, and May gets so angry she starts swearing down the phone.
The tragedy is a bit lessened by the fact that Gwen eventually gets better, in a very bizarre way.
The Clone Saga has several. May's heart-attack being one of them, but even worse is her yelling at Peter beforehand. She's basically his second mother, and all of a sudden she just starts saying these incredibly angry things and telling him to get out of her life, or the fact that when she has her heart-attack, Peter can't even do anything for her, much less get Nick Fury to help.
The reveal that nope, Peter's dad really is dead.
Harry Osborn's death. Even his father agrees he's gone too far at that point, and asks for someone to kill him. Too bad it didn't take.
Kitty's breakdown after the FBI try to arrest her, just for being a Mutant, and the fact that she fights her friends, lecturing them for barely standing up for her.
And the reaction of her mother, who's just left alone in her house with no way to reach her daughter.
The aftermath of the Chameleons storyline. Gwen is so shaken by what's happened that she runs away.
Fortunately she comes back a few issues later, only to reveal what happened: She went to find her mother, who was living with a new family and didn't want to see her daughter. Gwen very quickly breaks down into tears.
In Ultimate Spider-Man when Spider-Man dies. Crosses into Fridge Horror if you believe that both the Ultimate Peter Parker and the Mainstream Peter Parker share many of the same traits.
All of Ultimate Fallout. Everyone's reaction to Peter's death is emotional. Captain America QUITS over it, Nick Fury also feels responsible, and the city of New York mourns, to the point that thousands pay their respects at the funeral.
Mary Jane: "What are you going to do to me...?" Nick Fury: "I loved him." Mary Jane looks at him in shock. "I met him when he was just a baby. His parents were working on a project for us." Mary Jane: "You knew his parents?" Nick Fury: "Yes." Mary Jane: "I-I didn't know that." Nick Fury: "When his parents died, I wondered if I there was any way I'd be able to do right by them. And then I was so excited when he had the accident that gave him his powers. Now I could do something. I was grooming him, you know. I was so sure he would grow up to be the man his father wanted him to be and so much more. This brave, one-of-a-kind genius little boy. I should have taught him more, I should have slowed down the world so a boy like him could become the man he was supposed to become." Mary Jane: "I didn't know you knew his parents." Nick Fury pauses and she continues. "Okay I won't-I'm not going to send out anything I wrote. I didn't know.' Nick Fury: "I understand you're looking for someone to blame for this...my point is...you blame me...and I came to tell you...you're absolutely right.*tear goes down his cheek*"
The first Fallout issue is this for pretty much every page.
When Aunt May invites Gwen to live with her and Peter, and Gwen just throws herself into her arms and starts to bawl.
The lottery. Every single kid there is gifted, but whether they're going to get a decent chance depends on whether they're lucky enough to be picked from a lottery.
Miles' mother dying in his arms is heart wrenching. Made worse the next day when he wakes up to realize the nightmare was real.
Spider-Men features the exchange where 616 Spider-Man meets Ultimate Aunt May and Gwen Stacy. They're naturally asking lots of questions about their counterparts, and when Gwen asks Peter what she's like in his world, he hesitates for a moment, then just smiles and tells her that she's awesome.
What companies like Roxxon do to people like Spider-Woman or Cloak and Dagger all for the sake of the almighty dollar! i.e Tandy and Tyrone were just your average high school sweethearts who had their whole lives ahead of them, but after a near fatal car crash on prom night, they are spirited away to Roxxon industries where they are genetically tampered with against their will (the couple were somewhat dead following the car wreck but still) in an attempt by Roxxon to replicate the success of the super soldier serum much like Norman Osborn or Justin Hammer tried to in the past and if that weren't bad enough, people in this reality dislike (most) super powered individuals in this reality even more than in 616! As Jessica Drew puts it to Miles Morales:
Jessica Drew: (to Miles about Roxxon's true nature) "These monsters are going to try and try and try to remake you and me and Captain America and the Hulk...And they are going to keep trying and they don't care who gets hurt! They just want the money!"