How likely is it that the winner of the 2012 presidential election will lose the popular vote?

About 5%, according to Nate Silver at the New York Times:

One hypothesis might be that Mr. Obama enjoys some sort of intrinsic edge in the Electoral College — and that, like Mr. Bush in 2000, he could win the Electoral College while losing the nationwide popular vote.

Our analysis suggests, however, that this is not necessarily the case. The model’s simulations estimate that there is only about a 2 percent chance that Mr. Obama will win Electoral College while losing the popular vote. Meanwhile, there is only about a 3 percent chance that Mr. Romney will do so.

Silver forecasts that Obama has a 62% chance of winning re-election — much lower than the 80% chance that Obama would win if the election were held today.