I think the cup of sonics is meant to indicate all the iterations of the Doctor that were using the office at the university. Those were 'their' sonics, placed in the cup while they were off doing something else on earth/around campus - as if that office was a nexus where they all crossed paths in some way. This would explain why even the ones we've seen destroyed were present, as they hadn't been destroyed - yet.
Bill remarks, something to the effect, that "the Doctor" has been lecturing there "for fifty years or something." This would fit with all of them coming and going in and out of this timeline as they 'travel'.
It seems likely, as all versions were present (even the Eccleston/Tennant variants) - except 12's (he's got it on him) and the War Doctor's, who would not have visited the university.