Inspired by the rationalist Hamlet idea, I'm thinking of doing rationalist Romeo and Juliet some day (the way it would work is that Romeo is an instrumental rationalist while Juliet is an epistemic rationalist, and they bond over arguing and teaching each other stuff). But don't hold me to that; I'm notoriously bad at writing out cool ideas that get into my head.
I've been enjoying reading Less Wrong fanfiction, and I wanted to suggest another fandom that should have at least one rationalist fanfiction: Mage: The Awakening. It's a roleplaying game about "modern sorcery." My description can't really do it justice...