Doctors with pony companions: 2  
The Doctor was, after his encounter with Time Lord justice, obliged for a time to travel the universe at their behest, sorting out problems that they couldn’t muddy themselves with officially. His companion, Jamie McCrimmon accompanied him during this time. At one point, they found themselves thrust into an alternate universe populated solely by colorful ponies, and gained a new friend in the form of archaeology student Daring Do.  
I chose Daring to accompany the Doctor because… well, she’s interested in history and fighting evil. I chose the second Doctor for her fellow traveler because underneath his buffoonery, he really was rather ruthless, and as far as heroes in Equestria go, Daring is one of the most pragmatic and least likely to ‘hug it out’.