I think I've recommended this story before, but it's one of my favorites. Set in the "Smallville" TV show continuity, this fic tells us what might have happened if Clark's ship was discovered by Lionel Luthor (Lex's father on the show, and a deliciously evil villain in the first 3 seasons).

It's Elsewhere by bulbus. I love it, but then I've always been partial to alt-universe stories.