Kor Watkins wrote: "It was by Roy Thomas. I think it's also the only "What If" that's meant to be "in continuity". There's a What If trade paperback with this story in it."

The "in-continuity" issue of What If was number four, which posits a number of replacement Caps coming in to cover for the original's disappearance and subsequent hibernation.  It was this story which brought in the idea that William Randolphs (the Spirit of '76) and Jeff Mace (the Patriot) had both played the role in post-war versions of the Invaders and the All-Winners Squad.
The next issue was the "What If Bucky had lived?" story in which both Cap and Bucky survive and continue to age in real time after the war.
As I recall, What If 9 ("What If the Avengers had been formed in the 1950's?") also contained some language by the Watcher suggesting that their adventures may have taken place in continuity on the Marvel-Earth we all knew and loved.

What if the Red Ghost drove around in a pickup staging bare-knuckled prizefights?

What if the First Line had failed to stop the Skrull invasion?

Always wondered what would have happened to the heroes of tomorrow. I always thought that an underground movement of future heroes would save the day.

I have a post-apocalyptic Batman take I'd love the opportunity to try as an Elseworlds story ("Done and done," yes, I know.) And really, what with space warps being as they are, Superman's rocket could have landed on Earth at any time or place in history...Also, a Barry Allen perfectly attuned to and aware of the Speed Force could have been a very different hero altogether.  While I'm not a big fan of further shoehorning a retroactive continuity implant into established stories, a Barry with that level of power and speed, a sort of Alan Moore Swamp Thing in a Kanigher/Fox world, with a Kanigher/Fox sensibility seems like it could be fun.  The Flash never had an Elseworlds of his own, did he?

Other What If's:
What If Beta Ray Bill had killed Thor?
What If Mary Jane Watson had kept the sword of Red Sonja?
What If Spider-Man had married Gwen Stacy? (The turning point here being the death of her father.)
What If Spider-Man had given up being Peter Parker? (Aunt May passes away while Peter is dating the Black Cat.  With nothing much to hold him to his life in New York, he chucks it all and becomes the globe-trotting man-of-adventure the Cat imagines him to be.)
What If Spider-Man had failed to save Aunt May? (The wreckage from the Master Planner's undersea hideout knocks Spidey unconcious and the serum that he needs to save his aunt is lost. Spidey's greatest moment of triumph never happens and instead becomes one more instance of loss and irrevocable failure... How many of those can Spidey actually take?)
What If Sgt. Fury had become Captain America? ("Why are we wasting a soldier-serum on green recruits? Let's give it to someone who's already in the game and knows what he's doing!")
What If Ben Reilly hadn't come back? (He'd still be out there, for a while anyway... )
What If someone else had been flying the shuttle when the Phoenix Force manifested itself to save the pilot? (Again, not the way I'd like to do "Someone else becomes the Phoenix," but you work with what you have...)
What If Tigra had killed the Molecule Man? (Unlikely, but maybe she could have pulled it off... As she might have gotten a big power boost out of the deal...Like a Cosmic Cube, but with stripes! )
What If Bruce Banner had died in the Gamma explosion? (Zombie Hulk!! With no one driving, what's holding him up?)

Chad, I liked your USS Indianapoulos storyline!  Nicely thought out! The idea of making someone named "the Destroyer" a key figure in story of the Bombing of Japan is a nice one!

QUOTE: When I was 14 or so I wrote an awful What if? story which had Sabretooth becoming the Herald of Galactus.

I find this idea strangely brilliant.

It's fucking awesome.