1. Flight to the Finish
Out of all episodes so far in the series this is my favorite episode due to its excellent way of dealing with how to treat people with disabilities. The plot is great in my opinion, and my favorite Cutie Mark Crusader is featured as the main focus.
2. Lesson Zero
Lesson Zero is quite possibly one of the best character developments for Twilight other than fulfilling her destiny in Magical Mystery Cure. Plus the subtle introduction of her friends writing letters too. This was the first episode I ever watched of MLP, and I loved the new magic animations from day 1.
3. Magical Mystery Cure
Despite it being an episode that many hated due to the "Mary Sueishness" of the new Alicorn Twilight, I can honestly say hand down that this was an episode that would nicely fit the series finale spot in its feels. I just loved it from start to finish.
4. Applebuck Season
Probably my favorite episode from Season 1 hands down. I loved the character development for Applejack, and also the fact that she made many funny faces.
5. Pinkie Pride
This episode was crazy, nuff said.