3. Scaroth
From the wonderful mind of Douglas Adams, 1979s City of Death was always going to be special but its helped on its way by the inclusion of a suave, squid-headed alien Cyclops as its lead villain. His appearance already sets him apart from most other Who monsters but Scaroth also has a complex backstory and goal involving time experiments with chickens, a spaceship in prehistoric Earth and stealing the Mona Lisa and it all makes perfect (Doctor Who) sense when you see it!
2. The Dream Lord
Appearing in the Eleventh Doctor episode Amys Choice, Im forever confused why no one goes on about how great a villain the Dream Lord is. Ably played by the very versatile Toby Jones, the Dream Lord is an enigmatic, mercurial character who sets the Doctor and his friends in a trap where they have to decide whether they are dreaming or awake. Its a great conceit for an episode which is made all the more enjoyable by the Dream Lord popping up and poking holes in our 900 year old hero. It seems he knows the Doctor well. A little too well (See the episode for more).