∂³Σx²

According to the secret files created by the High Court of the Time Lords, the Doctor's true name was ∂³Σx². (PROSE: The Trial of Doctor Who) The word was also inscribed in the Tomb of Rassilon, (TV: The Five Doctors) and could be seen on K9 Mark 1's regeneration unit. (TV: Regeneration)

One account, which also depicted the High Court of the Time Lords, indicated that the Doctor's true name held a mystic importance that caused him to keep it secret. It was also unpronounceable to humans. This was true for all Time Lords and their names. (PROSE: Doctor Who and the Auton Invasion)

Behind the scenes
PROSE: The Trial of Doctor Who is the only valid story, as the Wiki defines it, that explicitly confirms that "∂³Σx²" is the Doctor's true name. The claim was also reiterated in Marvel Premiere 57, though, due to the non-narrative structure of that source, the Wiki does not acknowledge it as part of the DWU. However, this name has certainly not been widely accepted, as the Doctor's name is a contentious subject with aplenty of conflicting "names", such as "Doctor Who", "Theta Sigma", and "The Doctor" being some notable examples. Moreover, despite the few sources revealing that "∂³Σx²" is the Doctor's name, how to pronounce it, or even the relevancy of it, is undefined. So it simultaneously answers one of the largest questions in Doctor Who while also resolving absolutely nothing.

In TV: Regeneration, the regeneration unit that the name is inscribed upon is implicitly linked to the Doctor, with hints that the Doctor was the one who installed it.