First Doctor: Applejack
Second Doctor: Derpy
Third Doctor: Twilight Sparkle
Fourth Doctor: Lyra Heartstrings
Fifth Doctor: Fluttershy
Sixth Doctor: Rarity
Seventh Doctor: Rainbow Dash
Eighth Doctor: Pinkie Pie
Ninth Doctor: Spitfire
Tenth Doctor: Princess Celestia
Eleventh Doctor: Vinyl Scratch
Twelfth Doctor: Princess Luna

I only left out the War Doctor and the Valeyard for lack of a better comparison, not because I don't count them (I usually do in fact, count them).

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