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To date a Dalek ("The Stolen Earth"), Grace Holloway ("Doctor Who"), the Master ("Logopolis"), a Cyberman ("The Doctor Falls", although he held off the regeneration until "Twice Upon a Time"), and a group of Time Lords ("The War Games") are the only beings to actually KILL the Doctor (although he obviously regenerated all five times, and Grace did so unintentionally). If you subscribe to the 'Season Six B' theory, then the Time Lords have never succeeded in killing the Doctor, but a group of animated scarecrows has ("The Night Walkers" (TV Comic comic story)). The Rani also possibly killed the Sixth Doctor in "Time and the Rani", but this is unclear. Nobody No-one killed an alternate version of the Doctor in "A Death in the Family" (Big Finish audio story), and Ruth and the Time Lords kill alternate versions of the Doctor in the unbound stories "Full Fathom Five" (BF Doctor Who Unbound audio story) and "Exile" (BF Doctor Who Unbound audio story), respectively. River Song appeared to kill the Doctor in "The Impossible Astronaut" and later in "The Wedding of River Song", but this apparent killing was revealed to be a fake.