Write an episode set in early S1 where Lois tries to figure out Superman's secret identity and a lot of imposters come out of the woodwork and claim to be him , ala the scene with the Invisible Men. Then when Lois finally gives up her search, Clark tells her the truth (such as in this scene from the animated show:
Clark Tells Lois He\'s SM ), only to have her not believe him because she thinks he's just joking around or another imposter. It, therefore, becomes a running joke between them that Clark makes subtle jokes about being SM (i.e. explaining all his "how can I get the bomb without the rest of you getting shot" lines from FlyHard) and she scoffs at them.
I believe it would work funniest as a missing episode type story with Clark winking at the Reader at the end (not literally, figuratively... or since it's a story, would it be 'literally'?).