Yes. In at least four instances the Doctor uses the word 'hell'. Once in "The Three Doctors", once in "The End of Time", Pt 2, once in "A Christmas Carol", and once in "A Good Man Goes to War". Tom Baker's fluffing of his line to Davros in "Destiny of the Daleks" - slurring 'Stay back!' into 'Back off!' has led some fans to imagine that the apparant line - 'Spack off!' - is in fact a Gallifreyan insult., which is backed up by some novels. Several other novels have the Doctor being said to have sworn in Gallifreyan or the like. Also, in "...ish" (Big Finish monthly audio story), the Doctor says 's**t' to test out if the word censoring software that he had given to Peri worked (created to filter out the 'omniverbum', a sentient word that possessed people), but, since the software did work, it was censored.