Season 6 has got to be my favorite season of FIM , so narrowing it down to five episodes was hard for me.

5.Flutter Brutter — Sure, there's nothing likable about Zephyr Breeze, but I like this episode because of how Fluttershy was taking ZERO crud from her brother.
4.The Gift of the Maud Pie — Before this episode, we've barely seen much interaction between Rarity and Pinkie Pie, so them having an episode together was nice to see. Also Rarity's impression of Pinkie Pie was priceless.
3.The Crystalling — sigh Flurry Heart. You don't deserve to get as much hate as you do. I personally have nothing against Flurry Heart. This was also a nice start to Starlight Glimmer's redemption arc, with her first task being to reconnect with Sunburst.
2.The Saddle Row Review — I love the mockumentary style of this episode done through the Mane 6's interviews. Also, Sweep Sweep Sweep Sweep Sweep.
1.To Where And Back Again — This episode was… controversial when it first aired (I wouldn't be surprised if it still is). Sure it downgrades a bunch of characters who are otherwise capable of defending themselves into prisoners, but I'm willing to overlook that for everything else this episode presents. Instead of Twilight or the Mane 6 as a whole being the focus, a bunch of side characters (that just so happen to be reformed villains) end up being the ones who save the day.

Disclaimer: These "top 5" images are my opinion, so you're free to agree or disagree with them.