I think the series was originally meant to end at Season 3, which is why it only has 13 episodes while every other season other than the first one has 26.
 
5.Apple Family Reunion - While this episode is simply Applejack working hard to try to accomodate for everyone in her family, the fact that it’s hardly anything more than that is what’s keeping me from putting it any higher on the list.  
4.Games Ponies Play - While we were first introduced to the Crystal Empire in the episode named after it, we get to see what the place is like when there isn’t evil lurking around. Also, Ms. Peachbottom is adorably hilarious.  
3.Magic Duel - The Great and Powerful Trixie! makes a return. (I haven’t watched Boast Busters, Trixie’s debut episode, so I don’t really have an opinion on that episode.) I thought it was cool how Twilight was able to outsmart Trixie by using simple illusions.  
2.Too Many Pinkie Pies - x50 the Pinkie Pie = x50 the hilarity that ensues!  
1.Magical Mystery Cure - sigh This episode… If I recall, EVERYONE hated how Twilight became an Alicorn in this episode. Had this been the series finale, it would’ve been a nice summation of everything Twilight has learned up to this point.
 
Disclaimer: These “top 5” images are my opinion, so you’re free to agree or disagree with them.