The Doctor's Theme from series one is my favourite Murray Gold piece of all time. I get chills every time. The Doctor's Theme Series 4 was still good, but it didn't quite have the same feel as the original. So I chose Doomsday, which is my second favourite Murray Gold piece of all time. The Shepard's Boy is probably one of my favourite post-Series 4 pieces though.
Other greats include: Father's Day, Madame de Pompadour, The Daleks, Martha's Theme, The Rueful Fate of Donna Noble, and Together or Not at All.