53. "The End of Spider-Man!" Amazing Spider-Man #18-19 (1964)
One of the things that Stan Lee clearly always loved a lot about Spider-Man is the "everyman" nature of the character. This was perhaps never shown greater during the original Lee/Ditko run than the classic Amazing Spider-Man #18, where Spider-Man finally decides that he has had enough and decides to no longer be a superhero. This was the first time that Spider-Man quit since the launch of his series and it would be the blueprint for all other future versions of this theme (although one ended up being even more famous than this one). However, at the end of the day, Spidey's sense of responsibility is more powerful than anything else and he, of course, goes back to being Spider-Man just pages after giving it up "forever." This issue was famous, though, for how it was an entire issue that did not have Spider-Man face a single villain!
The next issue, though, Spider-Man makes up for the lost time from the previous issue by taking down the Sandman, who he just ran away from in the previous issue (thus making a lot of his fans turn on him, with only Flash Thompson and the Human Torch remaining believers in Spider-Man's honor).
52. "If This Be...MODOK!" Tales of Suspense #92-94 (1967)
This excellent action-packed adventure by Stan Lee, Jack Kirby and Joe Sinnott pit Captain America and Sharon Carter against Advanced Ideas Mechanics (AIM), who are introducing their new leader, MODOK, one of the most Kirby-esque creations of all-time!
While the introduction of MODOK is clearly the highlight of the arc, historically, the highlight of the arc when you are actually reading the comic is clearly the way that Sharon Carter is handled. Jack Kirby and Stan Lee definitely had an affinity for the scrappy young SHIELD agent, and they use her beautifully as Captain America's partner in crime on these action-driven SHIELD missions that Cap would go on as the driving narrative force of the late era of Cap's Tales of Suspense run going into the series being re-titled Captain America (it is still amazing how well the book evolved from having its story-length double when the book when from a split book to a fully Captain America series).
51. "Whom the Gods Would Destroy!" Journey Into Mystery #124-125, Thor #126-130 (1965-66)
After introducing Hercules with a brawl in the past, Kirby and Lee (and Colletta) then brought Hercules to the present for a rematch (although one that the two heroes don't realize is a rematch, since their memories were wiped of their original encounter), with the new fight now being set in modern times, with all of the stunning set pieces that you would expect from a battle through New York City...
While Thor/Hercules brawls are awesome, they eventually make up and become good buddies. This, then, leads to a story involving the villainous Pluto where Hercules and Thor must team up to take him down.