Howling:The clues lie in the shoes.

Keep in mind I haven't read any definitie spoilers, but while hanging over at TVTropes, I came up with something that... honestly seems to be fairly watertight.

Pay attention while watching The Rebel Flesh. The Doctor gets analyzed by the Flesh, then he goes outside and his shoes get melted by the acid. Which might seem silly at first, but remember, Gangers copy every cell, including clothing. Therefore, the Doctorgänger will be wearing the old shoes (and will be at least in that regard identifiable from the real Doctor.

But it's bigger than that. Now go back and watch The Impossible Astronaut and look at the Doctor's shoes. They are his original shoes, not the replacements. (He's even wearing the same bowtie.)  Which means that the Doctorgänger (with all the Doctor's memories intact) is the one getting shot on the beach, not our Doctor.

Which leads me to the conclusion that the Astronaut... is the Doctor.

Witoki 16:29, May 26, 2011 (UTC)
 * ...All the Doctor has to do is get a new pair of shoes after The Almost People. It's as simple as that. Just watch; by the time of A Good Man Goes to War, he'll probably have his regular shoes back. -- Bold  Clone  16:44, May 26, 2011 (UTC)
 * But see, it seems out of place to put as much emphasis on him losing his old shoes and getting new ones (including a closeup of the acidy ones, and the new ones on his feet) if they mean nothing at all. Add to that that the Doctor has an identical pair of shoes and grey bowtie and there is literally nothing to distinguish him from his Ganger self.  The dead Doctor doesn't even appear to have his TARDIS, he may have even been dropped off by the real Doctor just before. Witoki 16:52, May 26, 2011 (UTC)