Pretty much every CMC episode, especially Sleepless in Ponyville. I remember when I used to shudder at the mere thought of a CMC episode, and Sleepless was my main contender for the worst episode of S3 for a while.
I still find Scootaloo to be pretty annoying in Sleepless, but upon watching it again, I think there's definitely some great character development in there, Scoot and Dash becoming sisters opens up whole new worlds of possibilities for the characters, and the writers were actually pretty inventive in their storytelling.
For instance, one scene that I love in that episode is where Sweetie Belle and Apple Bloom are frightened by one of Dash's stories, scream, and turn to hug their big sisters, whie Scootaloo sat alone. I was even impressed by that scene even on my first viewing, and re-watching the episode makes me appreciate it even more. I guess I can't really condemn an episode for having one annoying character, when the storytelling and character development are nothing short of groundbreaking for the series.
Really, upon reflection, Sleepless is probably one of the best CMC episodes, only being beaten by the phenomenal Sisterhooves Social. That's how much that episode grew on me after only one repeat viewing.