Here’s one that always fascinated me. The Spidey figure on the cover of AMAZING SPIDER-MAN #35 is a Kirby figure (usually attributed to Ditko inks, but I never quite saw that). Don’t think it’s ever been reprinted in any other version in English (unlike some other covers with paste-ups which reverted in reprints), but someone dug up this foreign reprint. Click for a closer look at both covers.
(see comments for more, including a reprinting of the original in an English edition that I didn’t know about)
I will say that the modified version is the more attractive cover, with a great Spidey figure. I’m not sure exactly why the original was seen as needing altering, though. Too unflattering a pose for the hero? Did it make Spidey’s butt look too big?