There have been hints that the Doctor may have an identity other than the semi-mysterious one that the second Doctor revealed. That he became bored with the Time Lord ethos of staying home on Gallifrey and semi vegetating - the fourth Doctor alludes to the Time Lords studying all of history, but not remembering which century they lived in.

However, there were hints in Sylvester McCoy's Doctor that he was someone/something other than just good old Theta Sigma, frat boy. When he faced the Gods of Ragnarok, they claimed that they knew his secret, seemingly they knew of him in the "old times" (implication that he was someone else and played a major role in a previous universe). 

I am not sure if it was this episode, but in one of the seventh Doctor's final season, she asked the Doctor "Who" he really was. Of course, he doesn't answer.

That the Doctor had another, darker identity has been speculated about before... that he was involved with Omega/Rassilon in the earliest days of Gallifrey... or that he was the original foe that defeated & imprisoned Fenric.