Big Bad/Web Animation

"The ultimate villain of the story, who's causing the problem the heroes must solve."

Note that Big Bad is not a catch-all trope for the biggest and ugliest villain of any given story. The Big Bad is the one who turns out to be behind several other seemingly independent threats.

The Big Bad of Broken Saints fits this to a T, down to his identity being unknown until the brilliantly timed closing epigraph of the penultimate chapter: "'Tis the time's plague when madmen lead the blind." -- King LEAR
Super Mario Bros Z's primary Big Bad is Mecha Sonic, though Bowser and Dr. Eggman are a close second.
- Spoilers for season 2 shows the next Big Bad might be either Chaos 0 or Smithy using a revived Mecha Sonic as Axem Blue.
In Banana-nana-Ninja!: Banana Shop of Horrors, the Big Bad is I.R. Kostlowski, the manager of the PriceCo Supermart who refuses to stop selling bananas for food after hearing the banana ninja's pleas to free them. He engages Baninja in a pencil-to-tiny sword Boss Battle to defend his "best wholesale contract."
In KlayWorld: Off The Table, King Womp is this. When he and his fellow "aliens" (that is, peach-colored clay people instead of blue ones) come upon the Table's Klaymen, his reaction seems neutral... at first.

Womp: (makes his appearance, looks at the Klaymen) Wow. We've got a lot of stuff to improve here. (approaches Klaymen, folds hands behind back)

He proceeds to explain that his people journey all around the world, finding other clay civilizations and accepting them into their own... and says that the blue Klaymen are the worst.

Womp: ... I'm gonna be honest. You guys are probably one of the worst clay men we've ever run into. You're just blobs; there's nothing special about you. But I'm gonna do you a favor. I'm gonna cut you all apart, and we're gonna build you into something better.

The whole time, he has a scarily calm, reasonable, deadpan delivery (courtesy of Jason Steele) that sprinkles Nightmare Fuel through the Uncanny Valley.

The "Shadowy Figure" to Stinkoman from the 20X6 universe from Homestar Runner. Too bad we never see him...