The Doctor can be killed just like any other man. His only advantage is his regeneration, but if you can hold him in one place long enough to kill him the remaining number of regenerations, he will eventually die provided that there is no Gallifreyan intervention. There have also been several times in the show that The Doctor comes up against something that will kill him for good, such as the poison in "Let's Kill Hitler" or using his memory to help the computer in "Forest of the Dead". The best way to kill the Doctor, though, would be to simply find a way to deal a fatal blow to him after he has begun regenerating, apparently killing him for good (although the only time this has ever occurred or worked is in "The Wedding of River Song"/"The Impossible Astronaut" (Same attempt, two perspectives), and it was a fake death, so who knows?).
Man I hope I'm not talking to a Dalek =P