Hmm ... various sources that could be adapted for rationalist fic ...
Easy: Rationalist Mrs. Frisby and the Rats of NIMH. It's already got science, intelligence increase, and ethics (the rats' goal to "live without stealing"), so it's hardly much of a leap.
Medium: Rationalist Neon Genesis Evangelion. It's an incredibly ad-hoc story, laden with occult symbology; it's also involved with rather silly pop psychology (the "Hedgehog's Dilemma") and psycho-mysticism (the "Absolute Terror Field"). On the other hand, it's been heavily adapted for crossovers of all sorts already.
Hard: Rationalist Aqua Teen Hunger Force.
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...