A respiratory bypass system was introduced during the Pertwee era, which allows the Doctor to breathe in poisonous atmospheres. The Fifth Doctor was able to survive brief exposure to the vacuum of space (the Eleventh Doctor demonstrated this ability in the 2011 Christmas special too). I believe Time Lord body temperature is 60 degrees.
And of course, Time Lords are time sensitive. In episodes like "The Time Monster" and "City of Death", the Doctor and Romana were unaffected by time distortions that affected Humans. Time Lords are also telepathic. They can perform mind melds similar to Vulcans (eg "The Girl in the Fireplace"), transfer memories through head butts("The Lodger"), hypnotize people by looking into their eyes ("Terror of the Autons" etc.), and sense other Time Lords. Time Lords are also incredibly long lived, even when they don't regenerate. The First Doctor was over 400 by the time that he regenerated, and the Eleventh Doctor has already gone over 200 years without regenerating or even visibly aging.