One hypothesis is for the existence of different preferences, according to which women decide to stay away from higher rewarding jobs, sometimes because they prefere to take care of the family and children. Another hypothesis relates to the existence of a "glass-ceiling", which means women are excluded from top-level jobs because of gender discrimination. Some recent work by Daniele Paserman and Evren Örs et al. has investigated another hypothesis related to diverging performance under pressure. Women earn less because they are less effective than men at performing under stressful conditions.
Two psychologists at the University of Exeter have identified though another potential channel which may lead to the persistence of a wage gap. Haslam and Ryan (2008) show in a series of experimental studies that women tend to be over-represented in managerial positions which are more likely to end up as a failure or be subject to criticism. Basically, even if women manage to break the "Glass-ceiling", they will end up facing a "Glass-Cliff". Why would it be that a woman is more likely to be chosen to lead a boat when it's clear that the boat is sinking, it still remains an open question I believe. It seems though that the potential relevance of this hypothesis for any context which involves discriminated groups is undoubted.
Another interesting study from Judge and Livingstone (2008) at the University of Florida analyzes the wage gap within gender along a different dimension: the gender role orientation. Their finding is, that "traditionalist" men (those who believe women should stay in the kitchen, to put it bluntly) earn 8.459 $ more than "egalitarian" men. The reason would be that "traditionalists" are rewarded for their preservation of the social structure, while egalitarian will be penalized. Among women, instead, there is no such significant wage gap along this dimension, but only a wage gap vs. men.
Social Norms though are endogenous and change slowly through time, but policy action could be taken to foster such long term trends, hoping that sooner than later, the wage gap(s) will disappear and maybe revert (as I observe among some colleuages of mine here at the Institute...:-P)