Here are my picks for the top five most iconic covers featuring Red Skull (with iconic being determined by what covers are most established and most recognized when it comes to Red Skull, with a preference towards covers that are homaged a lot). This is not a BEST cover list and due to the very nature of icons, very few (if any) recent covers will be on the list. A notable exception to the rules is that I don't count covers from a character's first appearance (which isn't applicable to all characters, of course, just those who appeared on the cover of the comic they debuted in), as those tend to be automatically iconic so they're boring. Here's a list of all characters featured so far.
This is a tough one - the Red Skull has never been the most "cover friendly" character in Marvel history, plus he usually only appears in one comic book. But let's see what we shall see!
Artist: Gil Kane
The only comic book series to ever star the Red Skull!
Artist: Mike Zeck
A great cover for the 300th issue of Captain America - it really captures the intensity of their rivalry.
Artist: Marie Severin
I hate to have more than one "Skull with the Cosmic Cube" cover, but, well, that's pretty much what the Skull does all the time! And that's certainly an iconic Skull pose!
Arist: Alex Schomburg
Schomburg neatly provides the template for basically all of the Red Skull's Golden Age appearances with this cover (by the by, this was a different Red Skull than the one we all know nowadays).
Artist: Jack Kirby
An iconic cover that goes with what has become THE iconic storyline for the Red Skull.