Please note these are brief reasons and I have more favourites. It's hard to narrow it down with a show this good.
Dragonshy - Everything about this episode was great, but by far the best part was the ending. Seeing Fluttershy stand up to the dragon was great.
Winter Wrap Up - The whole episode was really good and it contains my favourite song.
Sonic Rainboom - I love the scenery and the ending is wonderful.
The Return of Harmony (both parts) - Discord was a great antagonist and seeing Twilight rise up and save her friends and ponyville was a blast.
And of course the mane reason why I like most episodes (watch the show) is because of the mane cast. I like lots of things about lots of episodes, but the mane cast always comes out on top.