The following is a ranking of every TV story from Pertwee's era. Feel free to comment what you agree or disagree with and how you'd rank these stories.
1. The Sea Devils (Possibly the best Master story in Doctor Who as a whole)
2. Frontier in Space (One of the best examples of the range of ideas Doctor Who can do. This story features really well realized political conflict and is the last appearance of Delgado's Master)
3. The Three Doctors (not without flaws but I'm willing to forgive it a lot)
4. Carnival of Monsters (This was one of the first classic stories I ever saw)
5. The Green Death
6. The Time Warrior
7. Spearhead From Space
8. The Daemons
9. Terror of the Autons
10. Planet of the Spiders
11. The Claws of Axos
12. Inferno
13. The Monster of Peladon
14. The Mind of Evil
15. The Ambassadors of Death
16. The Curse of Peladon
17.Doctor Who and the Silurians
18. Colony in Space
19. Invasion of the Dinosaurs
20. Day of the Daleks
21. Planet of the Daleks
22. Death to the Daleks
23. The Time Monster
24. The Mutants