My top three episodes of the season were here, so I'll just say why I like them best.
The Last Roundup - Not even counting Derpy, the episode overall is fantastic. All the characters get their own nice moments, and the chase scene at the end is fantastic. Probably one of the funniest episodes of the season too.
It's About Time - I'm a sucker for a good time travel episode, and this delivered. All the small bits really added up, and the final act with Pinkie, Twilight, and Spike is fantastic.
Hurricane Fluttershy - This was great just because it felt like a smaller story than usual. This season has definitely been more out there than the first season, and this episode was just a small character story between Rainbow and Fluttershy, and it was done perfectly. A real highlight.