Lol big change, Magical Mystery Cure going from 13 to 1. Why such a bad first impression? I'll probably post my own list shortly.
List time GO 1. Sleepless in Ponyville 2. Magical Mystery Cure 3. One Bad Apple 4. Magic Duel 5. Apply Family Reunion 6 & 7. The Crystal Empire 8. Too Many Pinkie Pie's 9. Games Ponies Play 10. Spike at Your Service 11. Wonderbolt's Academy 12. Keep Calm and Flutter On 13. Just for Sidekicks Overall, I'd give season 3 a 10/10
Sleepless in Ponyville is just such a perfectly done episode. It ranks right up there with Sisterhooves Social as one of my favorites episodes in the entire series.
Sleepless in Ponyville is the second best Season 3 episode but Magical Mystery Cure is stilll my favorite Season 3 episode though.
One odd impression I've had for Season 3 - and I haven't read everyone's post, so I don't know if this has been stated before - but it almost felt like they were wrapping up the season. Things got settled with Trixie and Discord, Rainbow seemed to be making progress on her goals, Applejack seemed to be taking over more of the family affairs, and Twilly - well, we all know what happened there. It almost felt like they were afraid there wouldn't be a Season 4, so were planning on one last season. Or maybe it was just because it was so short. I dunno.
I love all the episodes. All the episodes ever. Except the one with Discord and the Maze. Yeah. But I can't say, that I hate any episode. That'd be ridicolous.