Ultimate Spider-Man/Heartwarming

Nick Fury comes with a squad of Spider Slayers to take Peter, and the Fantastic Four arrive to help Peter.

Mr Fantastic: Why don't you tell us what is going on here? Peter Parker has done nothing wrong.
Nick Fury: Well, I'm kind of in the middle of a domestic military operation, Richards. So follow my direct order and go home!!
Human Torch: Yeah, well, I have like three friends in the world. You aren't doing this to one of them.

Peter and MJ have "The Talk".
One of the most shocking and heartwarming moments comes from Ultimate Marvel Universe's Scrooge, J. Jonah Jameson. In the midst of Ultimatum, with New York destroyed by a tidal wave and countless thousands dead, Jameson and the Daily Bugle staff are holed up in a shelter in New Jersey. As everyone else is calling loved ones or despairing, Robbie approaches Jameson, who launches into a broken, melancholy speech about how he was completely wrong and Robbie had always been right. In the midst of the devastation, Jameson looked out of his office window to see Spider-Man dive into the flood to save a drowning woman, and the journalist was overcome with shame and self-loathing. Jameson, who is characterized by hubris, admits to his faults and proclaims Spider-Man a true hero. A Tear Jerker at the same time, seeing the man so broken and pitiful.
After Peter takes a bullet for Captain America (Who gave Peter a "The Reason You Suck" Speech over his lack of maturity the last time they spoke), Peter remarks that Cap must think he's a complete idiot for doing that. Cap responds by pointing out that Peter just took a bullet to protect someone else, and tells him that "when you grow up, you'll be the best out of all of us."
From the Death of Spider-Man. This image. Also a Tear Jerker.
Peter's Funeral in Fallout. A city block and a half of spontaneous mourners, and likely more massed off-page.
- Issue #2 shows us that Thor, while sad that Peter isn't among the living, smiles because he knows that Peter's soul has ended up where he deserves to be... The Heroes Banquet of Valhalla, the Ultimate Marvel version of Heaven for fallen heroes. What makes it extra heartwarming is that he's not the only hero there. Doubles as a Tear Jerker if you take it as Thor simply imagining things.
From Fallout 6, Nick Fury admitting to Mary Jane that he loved Peter and that it was his fault he died. I think I have something on my eye
After Spider-Woman takes Miles into S.H.I.E.L.D custody, Nick Fury & Tony Stark both call him out on wearing Peter's costume, as expected considering they both liked him. But who else does this? Hawkeye, who's few interactions with Peter involved Clint being a Jerkass to him.
There's also the rather cute image of Nick Fury escorting Miles around the Triskelium, holding Miles hand the whole time.

Ultimate Spider-Man, Animated series.

The little Flash Back in "Great Power", to when Peter and MJ were best friends as kids. Talking about how they "ran away forever (being unable to cross the street, they just walked up and down the driveway)" and how they decided to finally "get serious" when they were 12, kissing and immediately going "eewww!" at the same time seconds after. It's really sweet to see that, and to see how they're still best friends to this day.
- And again, when Peter flashes back to how he first met and became friends with Harry Osborn. Harry and Norman picked Peter up when his bike broke down in the rain, giving him a ride back home. Norman hoped Pete would be a good academic influence on Harry, something he wasn't too keen on. Then Pete started to talk about his Uncle and how he really took care of him and wanted what was best for him. This made Norman genuinely smile, something Harry had always wanted to see.

Harry: He's smiling. My dad is actually smiling! (Turns to Peter) How'd you do that?
Peter: It's a gift.
Peter (narrating): And since that day, we've been best friends forever.

In "Doomed," Fury gets majorly angry that one of them dragged the team into a fight with Doctor Doom and nearly destoryed both the Helicarrier and New York. He says that the one responsible should step forward, because they're off the team. Spider-Man goes to take the rap, and just as he does, the rest of the team does with him. Sure, they may fight, they may get on each other's nerves, they may drive each other crazy, but when it comes down to it, they're a real team. They stick together, and they stick up for each other. Fury's response?

Fury: Don't ever let it happen again... (Smiles) Team.

In "Venom", even after Harry's hurt by how Peter's been spending more time with his "new friends", when the Symbiote's on the loose in his apartment, he repeatedly asks about Peter and whether or not he got away safely. Likewise, it's seeing Harry that gives Spidey the willpower needed to break free of the Symbiote.
The Hulk in "Exclusive": "Humans! Stupid Except for Bug Man! Bug Man good smasher!"
Can we just say all of The Avengers' interactions with Spider-Man? Iron Man, Hulk, Thor, and probably Captain America (comics) once he makes a guest appearance all treat Spidy like a kid brother and by the end of the episode appreciate and admire him.