What episode of MLP do you consider a bit dark (or rather phrased as "not best for kids") for the show?

I'm not sure. I guess, out of all the episodes I've seen, I'd have to say the Crystal Empire. There were ponies in chains, and King Sombra died.

Season four episode one and two. In the memory it looked like Celestia died. Twilight was even crying. Also when the mane six where going to that tree AJ said that Twilight should stay behind because she might get hurt or worse. That was pretty deep and I don't think A lot of kids would get that.
Also when they referenced Big Lebowski. That was epic.

If you compare this show to Adventure Time, even the darkest episode is still all sunshine & rainbows. The same could be said comparing Adventure time to Invader Zim.

I was watching Aeon Flux & A Nightmare on Elm Street when I was at this show's target audience age, so I'd say "none of them."