Discord did the most damage

Mostly King Sombra.

Discord was more into fun and pranks, it wasn't really chaos I mean, chocolate rain and flying pies are chaotic? That sounds more of pranks than chaos.

Queen Chrysalis was pretty evil, but even though she was basically helping her kind, she got defeated by the thing that gave her power.

King Sombra enslaved an entire empire and made the crystal ponies suffer with misery and were slaves.

Nightmare Moon, well if she succeeded, then yeah, she would make everyone suffer since there will be no warmth in the world and always nighttime and such. Besides, she might even start to take over empires for just more power.

Trixie didn't do shit, yeah, in the new season, she only took over Ponyville, and without that amulet, she's nothing.

I eliminated Trixie on the grounds that she's not really a threat. After that, it was a coin-toss between the two villains I actually knew anything about: Discord or Nightmare Moon.

Discord, out of pure awesomeness. XD

Chrysalis was the most badass villian so far, she was seriously evil and unnerving Discord was a fun character but kind of sucked as a villian, he seemed more interested in playing around than doing evil deeds, Nightmare Moon was boring as shit, King Sombra barely got any screen time and we barely got to know him

You can't compete with the living embodiment of chaos itself.

I voted King Sombra because you asked "Most Villainous" and not "Most Developed/Best Villain" or something like that. Sombra is the most villainous because he enslaves the whole Crystal Empire (essentially giving him all of Equestria under his control) and when Celestia and Luna take it back, he just makes it disappear for a thousand years, which is crazy when you really think about it.