Really didn't like the Shakespeare Code? That's been much higher for me. Why not then?
I do agree with the top 2, really hard to choose between them. Blink is so utterly perfect, even for people who don't know Doctor Who. There's a great line Russell T Davies said about Steven Moffat, "I gave you a two-parter and it was the best in the season, so I cut you down to one episode and it was still the best, so I gave you the episode without the ****ing Doctor OR companion in it and you STILL bloody made the best one in the entire season!"
What I loved about series three was the big build up to the Master's reappearance, all this talk of Harold Saxon. The Master's always been one of my favourites, and the emotional flashback with Gallifrey is lovely.
Season Four, despite Donna Noble being back, is actually my favourite season overall though I think. Donna redeems herself amazingly. First episode as usual, is ****, and then it just picks up.