It doesn't explicitly promote rationality, but in terms of demonstrating rationalist virtues in action I believe that the Stargate franchise, or at least the parts I'm thinking of* do a pretty good job. It strongly emphasizes curiosity, both for its own sake and in an instrumentalist knowledge = power sense. Secondly, there are large amounts of seemingly supernatural events that are reliable shown to be explainable by non-supernatual means. Admittedly the phelmtonium involved sometimes advanced enough that it effective works a magical black box, but its made clear that this is a property of the protagonists' rather than inherent to the phelmtonium. Lastly and far from least, most characters actually learn from their own and others experiences then modify there behavior accordingly. Furthermore, how good they are at this is one of the strongest factors in how effective they are. It does have some weakness, for example the characters are somewhat prone to generalizing from fictional example, but I think it comes out as a net positive.

*More or less all of SG-1, including the directed to DVD movies and the parts of Atlantis that I've actually seen.