I recently saw the new Batman movie, which is quite good. Overall, I have a much more favorable view of the Batman mythos than of the rival Superman series. Unlike Superman, who often seems to waste his immense powers on relatively minor villains, Batman/Bruce Wayne pays attention to the importance of opportunity costs. For example, he goes after the bigwigs of Gotham organized crime, not the smalltime petty thieves. He consistently attacks the most powerful villains he can realistically take on with the resources available to him.
The Batman story is also an interesting quasi-libertarian commentary on the shortcomings of government. Like the Mafia portrayed in The Godfather, the necessity for Batman's sometimes dubious methods arises because of the government's failure to protect people and their property against predation. This point is effectively emphasized in both The Dark Knight and Batman Begins. In that respect, Batman is similar to The Godfather in conveying skepticism about government, its motives, and its ability to effectively fulfill even the core "minimal state" function of protecting the public against violent crime.
In two important respects, Batman's message is actually more libertarian than that of The Godfather. While the latter portrays private protection firms (such as the Mafia) as being basically similar to government in their predatory nature, Batman's crimefighting activities are depicted as being both more noble and more effective than those of the generally incompetent and corrupt Gotham authorities.
In addition, Mario Puzo was extremely skeptical about the ethics and motives of "legitimate" businessmen, whom he portrayed as being little different from the Mafiosi. By contrast, Bruce Wayne is a billionaire businessman and his control of Wayne Enterprises is viewed as essential to his crimefighting activities. At times, the Batman movies even hint at the possibility that big businessmen actually have a self-interested incentive to help provide the public good of reducing violent crime. After all, they stand to lose a lot of profit if high crime rates reduce investment and drive away their customers and skilled workers. Precisely because of the vast size of his firm, Wayne has less incentive to free ride on the crime-fighting efforts of others in providing the public good of crime control. He will capture enough of the benefits of crime-fighting to justifying investing in it, even if he has to pay a very high proportion of the costs himself.
SPOILER ALERT (Proceed below at your own risk, if you haven't seen the movie yet):
The conclusion of The Dark Knight has an additional libertarian twist: Throughout the movie, Batman hopes to be able to give up his vigilante activities once Gotham's government is sufficiently reformed. The end of the movie, however, shows that this hope is misplaced, and that the city government's flaws can't be fixed merely by replacing corrupt and incompetent officials with more idealistic ones. As a result, the city will continue to need Batman.
I don't claim that Batman is consistently libertarian, or that the creators of the movie and comic books deliberately intended to convey a libertarian message. But the most recent movies and perhaps some previous Batman stories do have some interesting libertarian themes.
UPDATE: In fairness, as Steve Teles points out in an e-mail, Batman himself may not have completely lost faith in government at the end of the movie. That may be why he continues to believe that Harvey Dent's image as a popular hero should be preserved (though the preservation of Dent's heroic stature may simply be needed to prevent people from losing hope, not necessarily because maintaining it will improve the performance of government). But whether Batman himself fully internalizes the lesson or not, the movie certainly conveys a strong sense that government's flaws can't be corrected merely by choosing competent and idealistic leaders. After all, it's hard to imagine a public official more competent and idealistic than Dent himself was in the first half of the movie. Yet he fails.