Real quick, a rules note: 1) Each season will have two episodes on the list, and one Christmas special. 2) In the case of a multi-part episode, only one episode will be put here.
Honorable Mention-Amy's Choice.
#13. School Reunion (Series 2)
#12. The Doctor's Daughter
The reason for it being here and it being low is simple. Jenny. On the one hand, the chemistry with her and the Doctor is great, and she reveals some usually unseen tragedy in the Doc. On the other, she disappears after this episode and is never seen or mentioned again. Seriously Moffat, add her back in the next season!
#11. Let's Kill Hitler (Series 6)
#10. The Impossible Astronaut (Series 6)
#9. Silence in the Library (Series 4)
#8. The Impossible Planet (Series 2)
#7. The Doctor Dances (Series 1)
#6. A Christmas Carol (Holiday Special)
#5. The Eleventh Hour (Series 5)
#4. Dalek (Series 1)
#3. Blink (Series 3)
#2. The Big Bang (Series 5)
#1. The Sound of Drums