In the earlier days of Spider-Man, he was allowed his great triumphs. His triumph at the end of the Master Planner arc to save aunt may's life is a great big ball of heartwarming on peter overcoming the odds to save his Parental Substitute.
The wedding of Peter and Mary Jane. Even though they both arrived late, it still went off without a hitch. No supervillains wrecking things, no objections, just a happy ceremony with all the supporting cast coming out to watch.
When Peter thought MJ was dead, he ended up lashing out and attacking the Hulk, while yelling how no one was ever going to hurt anyone he cared about ever again and how MJ was still alive, and the Hulk... basically just stood there and said:
Bug Man's wife dead? Hulk's wife dead too. Hulk sorry.
After going through trial separation due to everything she put up with, Mary Jane finally agrees to get back together with Spidey, with both of them promising to do better this time around... then One More Day happened...
It should be noted that Stan Lee has never put the characters through One More Day, and they remain Happily Married in the newspaper strip continuity, as well as in the Marvel Comics 2 continuity.
The Kid Who Collected Spider-Man was an short back-up story in an otherwise forgettable issue. Spidey reads a newspaper article about a kid who idolizes him and wants to meet him. Spidey goes to visit the kid. They talk, the kid shows him his (very impressive) Spider-Man memorabilia collection. The kid also asks him "how does Peter Parker get all those great pictures of you?" which Spidey kind of dodges (since he is Peter Parker), and pesters him to tell him his secret identity, which he refuses to reveal. Spidey then starts to leave... turns back... and explains that Peter Parker gets those great photos of him because... he is Peter Parker. And then takes off his mask. Spidey then leaves, and we see him standing on a wall in front of the building the kid was in, and a sign reveals it's a hospital. Spidey is unmasked, and the "camera" pulls in, and he's crying. And we see the rest of the newspaper article. The reporter writes that he really hopes Spider-Man sees the article, because the kid has leukemia, and his doctors say he has only a few weeks to live.
After the whole fiasco with the clones, and the return of the Green Goblin, and the loss of his unborn child, Spidey is finally getting back to his roots. As he patrols the city, he stops to harass J. Jonah Jameson one more time. But when he sees Jameson alone at his desk, hours after his employees have gone, still working late into the night, Spidey decides not to play his usual pranks. Instead, he taps on the window, eliciting an angry tirade from Jonah. Spidey then calmly says, "Jonah, it's late. Go home."
The Watcher is usually The Stoic, but this Christmas issue of Spider-Man... it's just so sweet, it made me cry! Here's the link: Small Miracles.
Issue #591 had the Fantastic Four regain their memories of Spider-Man's identity from before the One More DayReset Button caused everyone to forget who Spider-Man is under the mask. You can see it here◊, complete with a nice bit of foreshadowing towards Spidey joining the FF after Johnny's death.
From the Spider-Man: Fever miniseries, there's a sweet moment at the end where Spidey notices that he and Doctor Strange make similar hand gestures. Heartwarming in a corny way.
Nice small one. In Venom #18 (2012), Flash-Venom has to rescue Betty from falling to her doom, in a situation more than a little similiar to the famous Gwen Stacy one. They instantly do so, instinctively telling her to go limp and everything. It's obvious this is because the symbiote picked up on Peter's constant replaying of that moment while he wore it.
The final scene of Spider Island. After working together to save the world, Peter and Mary Jane take a moment to watch over the city.
Peter: Look at 'em, MJ. A whole city. And they all walked a mile in my shoes. MJ: No. Just the wall-crawling parts. Everything that really matters is still right here, tiger.
In the Big Time arc, May has used her new poltitical connections to get Peter his dream job at Horizon Labs. As Peter walks towards the door, a panel from Amazing #1 appears (where the recently-widowed May tells him to continue his studies so he could become a scientist). She then looks towards the sky and says, "He did it, Ben."
After Harry rescues Spider-Man in the nick of time in Spectacular #200.
Harry: I did it, Peter. Just the way... you would've done it. A real hero. Spider-Man: Why, Harry? Why'd you come back for me? Harry: Hey... what else could I do? You're my best friend.
The cover to the returning Amazing Spider-Man #1. After the debacle that was Superior Spider-Man, seeing Peter in the red-and-blues once more with the biggest smile on his face, you just can't help to be happy once more.
At the end of the original symbiote story arc, after Peter has managed to remove the symbiote using the church bells and passes out, its last act before (seemingly) dying is to move him to safety.
In the weirdest example of this considering the character, Carnage provides a slight example simply because the symbiote will stop at nothing to keep Cletus safe in defiance of whatever advantages a different host would have over him. At one point, It seems like Carnage has hit the top, after taking over Silver Surfer, the herald of the creature that instills fear in it's entire race on a genetic level. However, after learning that it's first host is on the verge of death due to a mixture of health complications and the sheer amount of time since they were separated, the symbiote scarcely thinks twice about abandoning the Surfer and all the power that would entail in favor of reuniting with Cletus.
Throughout Mark Millar's run, Spidey is put through all kinds of Hell - Aunt May is kidnapped; Jameson offers a massive cash reward to anyone who can learn Spidey's identity; an attempt to stop the Vulture's latest spree goes horribly, horribly wrong and lands Peter Parker in the hospital; Mary Jane's poor investments result in the Parkers verging on bankruptcy; the Venom symbiote is sold to an angry little virgin who goes on a rampage; and Spidey learns that there really is an honest-to-God conspiracy to make his life miserable, culminating in a battle with the Sinister Six as Spidey is desperately rushing to save Aunt May from a death trap. Naturally, by the end of it, Peter Parker is just about ready to quit... and then Aunt May tells him that there's an actual website that has calculated the number of lives he's saved over the years. It's a very large number.
In Spider-Man/Black Cat: Evil That Men Do, Black Cat can be seen messing with one of Jameson's "Spider-Man is a menace" billboards while she's having an inner monologue about her past with Peter. The next page shows the billboard now with one simple word written over it: "WRONG"
Amazing Spider-Man (2014) #16: Despite their companies competing over a contract, Liz Allen and Peter Parker still get along rather well...their employees... not so much.
After Betty Brant is mugged and injured, Peter tries to find her attacker, instead of going to the hospital to see her, but after he speaks with Aunt May, he decides to visit her and they spent the reminder of the night watching movies in the same did they did when they dated.
Spider-Man allowing Morbius to take some of his blood, with permission this time, after it turns out Morbius bought a vial of his blood to try to create a cure for the zombie virus his best friend Werewolf by Night is infected with, in Amazing Spider-Man #622.
Spider-Man: Let's get this over with quick, huh? I get woozy around needles.
Morbius: It's all right. I have apple juice.
Amazing Spider-Man (2015) #1: We find out that Max Modell, Peter's old boss at Horizon, willingly invited him back into his little family by inviting him to his wedding with Hector Baez. Even more, Peter is able to give him a wonderful wedding gift - turning the Parker Institute of Technology he invited Max to run into Horizon University, giving him back a piece of what he lost due to Otto's arrogance.
In #3 of the same run, Pete has bought the Baxter Building. Johnny Storm is not happy about this, and confronts Peter about it. When Pete finally gets Johnny to stop fighting, he shows him the building's lobby, which has a huge statue of the Fantastic Four and family - a way for people to know that the Baxter Building will always be home to the Fantastic Four. Turns out Peter bought the place because a bunch of other companies were trying to buy it, and he outbid all of them in order to hold onto it until the Fantastic Four are back. Johnny's response?
Johnny Storm: Until it does, I'm glad it's staying with family.
Even more important is that we, the readers, didn't yet know when this issue saw print why Sue, Reed, Valeria, and Franklin are missing. But In-Universe? Peter was involved in the Secret Wars and remembers, per Word of God that those involved will. So, whatever happened to them, Peter is reassuring not only Johnny, but the readers, that the others will be back, somehow, someday.
It's also worth nothing that Peter hired Alicia Masters to sculpt the statue. Who else would have done it justice?
Peter has Harry Osborn (now Lyman) working as his VP at the Baxter Building, as well as Clayton Cole (former low level henchman Clash). He believes in giving second chances, he says. When Clayton dons his Clash gear to stop the Human Torch from trashing Peter's office, Peter gives him a mild reprimand, but says he isn't going to fire him, although he says they will have a talk about it later.
Harry: That, Johnny, is why Peter is my best friend. He never gives up on me. I'm not an Osborn to him. I'm just "Harry."