What a lot of people forget, I think, is that Roger Stern did not begin writing Spider-Man with Amazing Spider-Man. No, he first worked on Spectacular Spider-Man on a number of issues, and they're quite excellent issues. Definitely recommended.
Of course, it does not compare to when he took over Amazing Spider-Man with John Romita Jr. on art.
Hooooo boy, now them's some comic books.
What really stands out for me is how little of the soap opera qualities that were present in Stern's run. You see, while Stern managed to have subplots for Peter, they were pretty low key stuff - but you would never know this, because Stern managed to keep the title so darned busy with action plots that you never NOTICED!!
However, at the same time, Stern also managed to keep a whole lot of humanity in the title, and in Spider-Man himself, which is marked by his most famous story, the Boy Who Collected Spider-Man, which is a manipulative as all hell story, with a dying boy who is Spider-Man's biggest fan sharing a moment with Spidey. Touching, heart-rendering, and so true to the character, it is a great story.
However, to encapsulate the run, I think I would pick the other famous story from Stern's run, the fight with Juggernaut. Spidey not giving up until he defeated the Juggernaut gave way to many other stories, specifically the Firelord fight and the first Morlun fight (not the one where the dude eats Spidey's eyeball).
Such a classic issue, and John Romita Jr.'s art certainly did not hurt matters.