Jumping_Over_Fences said:
Of course, I would love it to be just some random woman with no real connection to the Doctor other than they know each other an developed a friendship. With all the guessing and speculation, it would be brilliant if it was no one.
Frankly, I think this is the most likely explanation. Considering that her first appearance was nearly two years before Amy showed up, I don't think they could have planned for them to be the same person, and seeing as she's essentially Moffat's personal sub-plot, I'm not sure he would be willing to change that.
She must be someone important though, and I suspect she is/ was a Time Agent like Jack Harkness, or something similar, otherwise she wouldn't have the knowledge to work with the Doctor as she does. It's pretty heavily implied that they have a romantic relationship, what with her saying that Future!Doctor cried before she went to the Library, and her claiming to know the Doctor's real name. It's also all but outright stated in Flesh And Stone that she's going to kill him; I suspect that this will be because he's going to go mad again like in The Waters of Mars, because Future!Doctor clearly didn't hate her when she left for the Library.
We'll find out soon enough, I'm sure. Although the fact remains that a lot of the appeal of the character lies in the mystery, and once that's gone there may not be much left.
Of course, the ultimate dream outcome would be that she's actually River Tam in disguise.