Yay! Finally I can rec! I should note that I particularly like fics that explore Time Lord culture, biology, language, or general alienness. (Oh, and one thing you should know if you're going to read Doctor/Master fic is that they often refer to each other by their school names. The Doctor = Theta (or Theta Sigma). The Master = Koschei.

For creepy Time Lord history.

For creepy regeneration sex.

More regeneration sex + alien linguistics.

Not creepy Jack/Ten fic

versaphile has lots of good Doctor/Master fic. (Including an *enormous* epic-in-progress called "Praxis".)

dameruth has some awesome crazy Time Lord biology in her fic. this is probably my favorite.