Often you'll see covers paying homage to or parodying a famous comic cover. For example:
So, which cover has been...well...covered the most?
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I doubt anything is parodied as much as Action Comics #1, but Amazing Fantasy #15 (the first appearance of Spider-Man) is pretty iconic, too. This page shows several:
I think Fantastic Four #1 probably takes the cake - too many to embed them all but check out this website - must be a few hundred!