Tough call, but I have to go with The Pirate Planet if for no other reason than nostalgia. It was one of my first Doctor Who serials (I started off young so I can't recall what I saw first) and it's a ripping fun story. The Pirate Captain, Mr. Fibuli, a giant factory that devours whole planets, fantastic Douglas Adams script, K-9 vs. robot parrot, and of course, the lovely Romana I. What's not to love?
That being said, The Androids of Tsra is a close second. Mary was absolutely brilliant in four different roles!