1, The Daleks
2, The Tomb of the Cybermen (still one of my all time favorites but for this list I had to pick something and it's not my favorite Troughton story or that much better than a lot of his)
3. Inferno
4. Genesis of the Daleks (Good but honestly it's not in my top three dalek stories and probably not in my top ten Tom Baker stories)
5.The Caves of Androzani (Good but it's tragic this is the one that gets remembered and called the best story ever when he was also in Enlightenment.)
6. Vengeance on Varos (A great story but it's not his only classic )
7. Remembrance of the Daleks (As with most of these I'm not disputing its greatness but it gets over hyped)
8. N/A
9. Aliens of London/World War Three (Just very bad overall. It's cool Tosh is introduced, UNIT has a cameo and there's a pig guy but the Slitheen farting is just so dumb.)
10. Blink (I can enjoy a Doctor lite episode but Turn Left is the only one I'd call great Doctor Who. This is very good television but The Time of Angels/Flesh and stone is better in my opinion.)
11. The Rings of Akhaten (I know this is a divisive episode but I see a lot of people who rank it pretty highly and aside for a few brief moments and the speech at the end it is pretty meh)
12.Flatline (It just doesn't click with me the way it seems to do with some people. I do like a lot of the ideas..)
13. Rosa (I think Doctor Who should be used to communicate important ideas like what Rosa is trying to say but this episode is very boring, with a lame villain and very little interesting or surprising ever happening.)