Avoiding the usual suspects (Maybe not the best, but very good and/or very fun stories):
The Death of Jean DeWolff
The Origin of the Hobgoblin
The Birth of Venom/Vengeance of Venom
Spider-Man: Ghosts of the Past (Epic)
Thor by Jurgens and Romita Jr.
Hulk: Crossroads
The Death of Red Skull
Daredevil: Fall of the Kingpin (Well, there was a trade in the 90's
)
Silver Surfer: Rebirth of Thanos
Thunderbolts Classic 1-3 (Come on, Marvel, where's volume 4??)
Ultron Unlimited (Avengers Assemble vol. 2)
Doctor Strange: The Oath