What the title said. Of the entire series
My favorite episode is Twilight's Kingdom, because of the big combat sequence with Tirek, and the presence of Discord. As well as a certain headcanon I have regarding Tirek. Though I am considering putting The Cutie Remark above it due to the alternate futures. I'll have to watch them back to back sometime.
My least favorite episode is Equestria Games, because they'd been building up to them for as long as the Tirek fight (the two arcs even coinciding in Rainbow Dash's key episode), but it turned out to be a Spike episode that recycled the plot of Sonic Rainboom and Hurricane Fluttershy. The first was the first use of it, though quite OOC for the usually-confident Rainbow Dash, the second was to be expected of Fluttershy and my favorite Fluttershy episode, but third time's just a little repetitive, and of course the way Spike had to save the Crystal Empire was a little ridiculous. Sure, disabling the unicorns' magic to prevent cheating is reasonable, but the princesses should have kept their magic and been trusted not to abuse it, in case an enemy should attack. I thought Chrysalis was going to crash the games, despite my usual headcanon for her that I'll go back to if she's absent from the final.
...but I've only seen it once and I have a tendency to like some episodes better the second time around, so maybe.