Most of the time I take the heart/lung shot. It offers the highest percentage of a clean kill. If I take a neck shot, it is at the base of the neck at the shoulders. It has been my experience that this shot will anchor them in their tracks.
I wish I had a camera on the last doe I shot on 11-11-11. It was about 70 yards from me and less than 5 minutes left of legal shooting light. I was hunting near a nasty thicket and did not want that deer running into it. I took the neck, base of the shoulder shot and the deer disappeared. There were several deer running off after the smoke from my muzzleloader cleared, so I was worried I may have missed. When I got over to where the doe was standing, I found her piled up with all 4 legs completely under her body. She had dropped straight down. It was like the "hammer of Thor" had hit her!