I like this question, because it got me thinking about "what ARE some of my favorite Spidey stories?" I think what I found is that the overwhelming majority of my favorites are the ones where Pete grows from facing a true or personal struggle... or come from a time where it didn't feel like everything was specifically written to be collected in the (inevitable) trade paperback, or when things weren't over-spoiled online. I tried to discount the fact that my favorites are older because of "nostalgia," but the stories to me from "back then" just seemed to have more to them. I have favorites from all different eras (some of which have already been mentioned):
Amazing Fantasy 15
Master Planner Saga
Amazing Spiderman 39-40
Amazing Spiderman 88 - 90
Amazing Spiderman 96-98 ("And Now, The Goblin")
Amazing Spiderman 121-122
Amazing Spiderman 135-137 (Harry Becomes Green Goblin)
Spiderman Vs. The Rattler (from the 70's Spiderman News Paper strip)
The Wraith Storyline from Marvel Team Up 48 - 51
The original Carrion Storyline from Peter Parker The Spectacular Spiderman
Nova 12/Amazing Spiderman 171 (Photon mystery... no real "struggle", just "fun" for me!)
Who Killed Jean DeWolff storyline from Spectacular Spiderman
Nothing Can Stop the Juggernaut
Original Hobgoblin saga (ASM 238-251)
Kraven's Last Hunt
Death of Harry Osborn (Peter Parker The Spectacular Spiderman 200)
The Kid Who Collected Spiderman
Amazing Spiderman 300 (yes, Venom was pretty scary in his original outings...)
Amazing Spiderman 400 (one of the best. Ever. Hands down)
Spiderman: Blue
The Thousand
The first storyline with Morlun
There are probably others that I've missed, but these are the ones that came to mind most quickly. The most recent story that I would add to the list would be from Amazing Spiderman 698 - 700. I imagine what the impact would have been for me if the outcome of the story hadn't been plastered all over the place. No last-minute save for our hero, a shift in the status quo, etc.
Just my brief thoughts