Of the storylines from the past, of course you have to include the Coming of Galactus for one. I also like the one that starts, sort of, with the FF Annual #2 in the story where we first find out Doctor Doom is the ruler of a mysterious country called Latveria. In the end, Reed plants the suggestion in Doom's mind that he has defeated, zapping him into oblivion with the encephalo-gun Reed. Soon after, the Frightful Four is formed and defeats the FF, leaving them powerless. Meanwhile, Doom comes to realize that Reed had tricked him and returns to New York to get revenge. Daredevil drops by for a guest appearance to help the FF foil Doom's plans but it is Ben's sacrifice to become the Thing once again that saves the day. He leaves the team in anger and once again the Frightful Four return to take advantage of Ben's mental state. The Wizard uses his ID machine to turn the Thing against his teammates. If I recall, this is one of the earliest examples of Marvel using the long form of story telling because this spanned about 8 or 10 different issues. Classic Lee/Kirby at the peak of their collaboration.