Many, many between Peter and Mary Jane. Sadly, for people aware of how Quesada ruined it, they all can turn into Tear Jerkers. One of the best, when Peter and MJ get back together and because she wanted to be a bigger part of his life, Spidey introduces her to Captain America.
The issue where Aunt May reveals she's learned Peter is Spider-Man. What follows is a complete deconstruction of all the excuses writers have given over the years as to why he never told her, and shows exactly how a little old woman could raise one of the greatest heroes in the Marvel Universe. At the end, she gives her blessing, and he puts on his suit and swings off into the night feeling, for the first time, "not confined, but free".
The 9/11 issue had most of the superheroes who live in New York teaming up to help at ground zero. And a few supervillains; Magneto lifts some wreckage. Doom cries. After all... Even Evil Has Standards. For some, it was the narration. We don't care how close it came to being overblown; the fact remains that some of the wisest, most sane 9/11 philosophy came from Spidey.
In the Spider-Man #500 milestone Uncle Ben is resurrected for 5 minutes to tell Peter that he has lived a good life, and that he is happy for Peter.