I elsewhere linked Luminosity, a retelling of Twilight et al., and was encouraged to make a quick post mentioning a few examples of rationalist fiction.
So here's that.
Rationlist fiction is not terribly easy to explain, because rationalism is a word with many meanings and also one that sets people off. What I tend to mean by rationalist fiction is stories in which there are no so-called idiot balls, or if there are, they're explainable, understandable, and can fool the reader too. Read this. Note that this does not preclude characters from making emotionally-charged but non-optimal decisions, because that's not what rationalism is. Real, rational people get carried away by their emotions. There's a great writeup on that somewhere on LessWrong but I can't find it, sorry.
Anyway. I'm by no means an expert but I've read some stuff and here is that stuff.
HPMoR. Harry Potter and the Methods of Rationality by Eliezer Yudkowsky. Strictly speaking, it's fanfiction set in JK Rowling's universe, which tends to turn people off. HPMoR is an explicit attempt to teach LessWrong's version of rationalism in a familiar context (which requires twisting the plot of actual Harry Potter into almost unrecognizable oblivion). Premise: HPMoR Harry Potter is a) a child prodigy and b) raised by intelligent, kind people. At times clunky, often very funny and quite emotional. Good fiction on its own merit but the ethical/scientific/rational ideas aren't just shoehorned. [Should be finished by ~February.]
Ra. Serialized science fiction, and so well-written that it gives me hope for the whole genre. Intelligent antagonists, moral gray areas, lots of layers. Not overtly rational, like HPMoR; it fits the looser definition in that all the characters make intelligent or nearly intelligent decisions which fuel the plot. [Nearly finished.]
Luminosity. Retelling of Twilight, linked above. Same deal; characters are more intelligent, thus the plot is more interesting. Not nearly as heavy on rationalism etc as HPMoR, much more so than Ra. (Example: one primary point of departure is that Bella is in favor of everyone becoming vampires for the simple reason that death is bad and vampires are immortal. It's more complicated than that but the viewpoints of the author/genre certainly enter the story.) [Entirely complete.]
The Metropolitan Man. Retelling of Superman's origin story (or something -- not a comics guy) but with gray morals which make everything infinitely more interesting than the shitty Superman movie I watched a few years ago. [Complete; quite short compared to everything else on this list.]
Worm. Incredibly long serialized original fiction about superheroes, but not pie-in-the-sky everything is great superheroes. More like a Watchmen situation where superheroes are just something people live with and sometimes that kinda sucks. I'm still slowly working my way through Worm and only list it because it's mentioned in the same breath as HPMoR and Luminosity all over the internet. [It's 1.75 million words and I have no idea if it's finished. I think it is. So, kleinbl00, if you only have time for one of these, it's not going to be Worm because then you'd only have time for a fourth of it. Not that the others are much shorter.]