Okay, to be honest, I didn't 100% like Season 1, I just picked out episodes I thought were… "okay" at most. By contrast, Season 2 seems to improve a bit.

5.Sweet and Elite — In this episode, Rarity tries to befriend the upper-class ponies in Canterlot while making an outfit for Twilight's birthday. I really love how kindehearted and accepting Fancy Pants was. And who can forget Twilight's hilariously terrible dancing?
4.MMMystery on the Friendship Express — Who doesn't love a good mystery episode? I love how we get not one, not two, but THREE culprits who ate the Marzipan Mascarpone Meringue Madness cake. Also, "I wear false eyelashes!"
3.Secret of my Excess — Okay, to be honest, Rarity and Spike's interactions ALONE is enough to make me like this episode.
2.Read it and Weep — Okay, be honest, bronies; How many of you DIDN'T react the same way Rainbow Dash did to Daring Do when you first watched this show? (As in when you first heard of it, you reacted in disgust or something like that, but as you watched more episodes, you grew to like the series.)
1.Baby Cakes — It was refreshing to see Pinkie Pie at least try to be responsible instead of being the optimistic, happy-go-lucky pony she usually is.

Disclaimer: These "top 5" images are my opinion, so you're free to agree or disagree with them.