Fun idea! Here's my list:
1. The Eleventh Hour
2. The Shakespeare Code (hey, I thought it was hilarious!)
3. Victory of the Daleks
4. Time of the Angels
5. Flesh and Stone
6. Dalek
7. Unicorn and the Wasp
8. Father's Day
9. Cold Blood
10. Vincent and the Doctor
11. Turn Left
12. The Pandorica Opens
13. The Big Bang
Special: The Runaway Bride
Wow, you were right, some of them were tough! There were times I had to choose among 3 or 4 that I really liked. None of season 2 made my list as even a contender. When in doubt I went with the Eleven cuteness factor (like #3, I thought all of them were pretty mediocre).