Well, for my own experiences and memories...
The first series of book, which had a deep and fundamental effect on me as a young child (when I was like 8 years old) is a series of scifi/fantasy books written by a Belgian writer (no idea if they are translated to English) called Philippe Ebly. Not his books contain any really deep message, it's just groups of teenagers having adventures, but those books deeply affected me because they are those which made me a book-eater. It's the first time I spent a whole Sunday devouring books.
Then I started much more of science-fiction, mostly from French writers like Christian Grenier, Jules Vernes and René Barjavel. I think that latest are the ones who influenced me the most at that time - Jules Vernes for his focus on science and the "miracles" of science, his heroes being engineers or scientists, more than anything else. And Barjavel for the ethical implication of technology and the sheer horror of war (especially in La Nuit des Temps ).
Later on, as a teenager, I also got very deeply impressed by Isaac Asimov, the Robots and the Foundation cycle. The scientific, rational approach of human societies that constitutes Psychohistory had a great call to me (even if I'm aware it's scifi and not fully realistic), into the power of reason, and the fact it can be used for anything, including improving the social structure of the society. And the way the Zeroth Law is devised by the robots in "Robots of Dawn" and "Robots and Empire" really struck me as a great analogy to how humans can, from selfish and stupid evolution, build an ethical system. The last sentence of "Robots and Empire" (hrm, I've only the French version with me, but re-translated from French to English it would be something like « And he was alone... alone to protect a whole galaxy. »), read as a teenager, played a very significant role in giving me something to protect. That, and LOTR message that « even the smallest person can change the course of the future ». Of course, those were teenage dreams, I'm aware things are not that easy in real life. And that many who tried to change the future did, but not in the way they excepted at first. But still, this teenage message is the foundation of what I've to protect.
But, more than any specific book (even if those books did play a huge role) I think that it's the huge number of books I devoured that shaped me. Each book forces you to identify and empathize with very different characters - a robot there, an alien here, a young slave there, a young prince here, a normal person who unwillingly become an hero there, a normal person who just ends up being convinced of a crime he didn't commit here, a really guilty criminal who still his a person with feelings, love and suffering there, ... That really did a lot to my ability to empathize with real-life humans, to not be too quick to label someone "evil", to try to understand people's real motives and ways of thinking before judging them, which is a fundamental thing if you want to be able to steer the future without completely botching it.
Follow-up To: On the Care and Feeding of Young Rationalists
Related on OB: Formative Youth
Eliezer suspects he may have chosen an altruistic life because of Thundercats.
Nominull thinks his path to truth-seeking might have been lit by Asimov's Robot stories.
PhilGoetz suggests that Ender's Game has warped the psyches of many intelligent people.
For good or ill, we seem to agree that fiction strongly influences the way we grow up, and the people we come to be.
So for those of us with the tremendous task of bringing new sentience into the world, it seems sensible to spend some time thinking about what fictions our charges will be exposed to.
The natural counter-part to this question is, of course, are there any particular fictions, or types of fiction, to which we should avoid exposing our children?
Again, this is a pattern we see more commonly in the religious community -- and the rest of us tend to look on and laugh at the prudery on display. Still, the general idea doesn't seem to be something we can reject out of hand. So far as we can tell, all (currently existing) minds are vulnerable to being hacked, young minds more than others. If we determine that a particular piece of fiction, or a particular kind of fiction, tends to reliably and destructively hack vulnerable minds, that seems a disproportionate consequence for pulling the wrong book off the shelf.
So, what books, what films, what stories would you say affected your childhood for the better? What stories do you wish you had encountered earlier? If there are any members of the Bardic Conspiracy present, what sorts of stories should we start telling? Finally, what stories (if any) should young minds not encounter until they have developed some additional robustness?
ETA: If there are particular stories which you think the (adult) members of the community would benefit from, please feel free to share these as well.
ETA2: My wildly optimistic best-case scenario for this post would be someone actually writing a rationalist children's story in the comments thread.
ETA3: On second thought, this edit has become its own post.