The best story with Spider-Man inspiring the city may be Spider Island, in which everyone in Manhattan gains spider-powers and Peter Parker finds a way to stand out when everyone has great power.
Ends of the Earth (Amazing Spider-Man #682-687) is a Sinister Six story with dramatic weight, loss and high stakes.
Amazing Spider-Man #617 and #625 have a standout Rhino story, as new villains try to force the retired Rhino back into the suit with tragic results.
JM Dematteis's Spectacular Spider-Man run (#178-200) is the best comic book version of the downfall of Harry Osborn.
The basis for the film relationship between Peter & Gwen may be Bendis's Ultimate Spider-Man, which essentially reimagined the Spider-Man comics as an excellent 21st Century high school drama.