The two-part episode A Canterlot Wedding, Part 2 is my most favorite episode of the show, and an epic, Disney quality episode with a dark Knight of Cerebus for a villain. (spoilers follow)
Queen Chrysalis is my most favorite villain in the show. She's darker than Discord, cooler in appearance than Sombra, has her own song (the second verse of which is particularly sinister), and there's some good Harry Potter references in there with Celestia vs. Chrysalis being like Harry vs. Voldemort, and the changelings shattering the barrier is like when Voldemort does it to the barrier around Hogwarts. And (major spoilers) I THINK Chrysalis and her army go out in true Disney fashion, but since it's depicted in a Team Rocket style there has been much debate, and other fans love her so much they want her to survive. Chrysalis's dark tactics, as well as the epicness of the episode, further prove that this show is enjoyable for all audiences
Although in Part 1, what Chrysalis does to Twilight, getting her friends, Celestia, and Shining Armor, all of whom have powerful relationships with her, to disown her of their own accord, was the single most depressing moment in the show. This is one of the reasons I want Chrysalis to be killed from her fall, even though she's still my favorite villain.