Family Appreciation Day- Everyone seems to forget about this one. However, I love it. There's a good amount of world building, and actually gives Granny Smith some character, with her and Applebloom's relationship getting some development. It also has some really great visuals and music.
Hearth's Warming Eve- This episode tends to be somewhat ignored by the fanbase, while I personally find it a really. really good episode. It provides a lot of world building, and tells a very interesting tale that fits within the context of the world, and actually does the racism moral properly.
It's About Time- First of all, I am biased as hell. I can REALLY relate to this episode. I, like Twilight, tend to worry myself over things in the future. The moral was really great. Also, Pinkie was awesome here. Madame Pinkie was hilarious, and I loved how Pinkie was really trying to help Twi, even if she was oblivious, and immediately tried cheering her up when Twilight realized what she had done after time traveling. It also kinda teaches two morals, with the subplot of Spike eating ice cream. Twilight learned not to worry too much about the future, but Spike learned that he shouldn't just act like the future doesn't matter.
The Crystal Empire- Why does this opening get so much hate? I really don't get it. Season Three was very much a finale for Twilight's journey from Celestia's antisocial, paranoid student to a leader who understands friendship. This opener shows this, as she is willing to "disobey" Celestia for the empire, while before she was willing to brainwash ponies so she didn't disappoint her. Spike also got to actually save the day for once, and it showed just how much Spike loves Twilight when he looked into the door. That scene, honestly, did what Owl's Well that Ends Well did, so, so much better. Sombra, while not really doing much, was a true threat. He planned everything out, wasn't defeated by his own pride, and managed to keep the Crystal Ponies down. He represented fear and sadness, and used it as his weapon, making sure to haunt the Crystal ponies so they couldn't defeat him with their positive feelings, and used it against Twilight and Spike. He wasn't another large ham, but a much more "behind the scenes" villain, and I love it.
Just for Sidekicks- I don't get why so many people dislike this one. Not only is it quite funny, but Spike acts like an asshole who cares more about a cake than the pets his friends trusted him with, and the episode actively punishes him for it. He also was refusing to even learn the lesson, which also makes his punishment quite justified. He was bringing a good amount of it on himself, and even after he learned his lesson, he still pretty much deserved what he got at the end. Plus, Angel in this episode, while a selfish asshole, does seem to actually care about Fluttershy.
Magical Mystery Cure- Yes, this episode was rushed, and should've been a two parter. That doesn't make it bad. First, in this strange world where they got their cutie marks in different fashions, they were never able to see who they truly were ("I don't really know anything about animals-Fluttershy). Meanwhile, the song "A True, True Friend" shows how friends can show each other paths they could not see before, and realize things about themselves, making them truly happy. The message of that song is really great and sums up the message of the entire show perfectly. Also, Celestia's Ballad. Like I said, Season Three was a finale for Twilight's journey, and this episode was a great ending, showing Twilight's growth and understanding as a character. This song really did show that, and made me very, very proud of Twilight, through a downright beautiful song. By the end of the episode, I actually was tearing up. It was just that...amazing.