"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.
Adventurers! played around with this, even having a PR war between two of the villains over who was going to be the Final Boss.
While it's not quite a certainty yet, a true Big Bad seems to finally be shaping up in Erfworld: it's probably Charlie. This page◊ (WARNING: MASSIVE SPOILERS) certainly goes all-out with the Shout Outs to drive the idea home.
JackNoir for Acts 4 and 5, helping to send Sburb severely of the rails.
VriskaSerket was thought of being the Big Bad of Act 5, engineering most of what took the game off the rails until it's revealed that she and several others were being manipulated by DocScratch, the realBig Bad of Act 5.
Her ImperiousCondescension for most of Act 6, controlling the Post-Scratch Earth and antagonizing the Kids although she's somewhat been out of focus upon the reveal of the psychotic, bloodthirsty Caliborn.
Lord English though can be seen as the Big Bad to the series as a whole given that he is the Bigger Bad to everyone else previously mentioned but has not made his first full appearance until just before Act 6, and has not yet encountered any of the main characters.
Though the comic also features Nale and Kubota (two Big Bad Wannabes), Redcloak (a Dragon who is in some ways even more dangerous than his boss), The Snarl (an Eldritch Abomination that hasn't done anything yet but could destroy the universe if released), Tarquin (the Magnificent BastardEvil Overlord who's also a main character's father), and the Interfiend Co-operation Committee (a trio of fiendish Chessmasters who are playing everybody else to a greater or lesser extent) — so there's definitely more than a bit of a Big Bad Ensemble going on rather than just Xykon. As he's arguably the most powerful non-divine villain in the comic and is the most central single villain to the plot, he'd still qualify as theBig Bad though, barring a (not entirely impossible) future upset.
Recent developments as of #830 mean this might be more of a Big Bad Duumvirate between Xykon and Redcloak, with each thinking they control the other.
Problem Sleuth had Mobster Kingpin, who was set up to be the game's Final Boss from the start. The heroes spent more than half of the game fighting him.
Sluggy Freelance: Hereti Corp and K'Z'K constantly take turns being the overall Big Bad of the comic. Other examples (mainly for mini arcs) include vampire queen Lysinda, demon general Lord Horribus, corrupt nobleman Sir John Jacobs, and a totalitarian dictator known only as "His Masterness".
Though His Masterness turned out to be a subversion. It was originally Alt Doctor Shlock keeping the people of 4U city in drugged stasis while he repairs the damage caused to the Dimension by his irresponsible portal abuse, then the role was assumed by Alt Riff who continued the job after Shlock's death, and then by a computer Riff left in charge of the city, while he devoted all his energies to saving the world, that ended up going rogue.
Xaneth of True Villains, being one of the main characters and leader of a villainous band, seems to be this as of now.
With this pageVoodoo Walrus seems to be setting things up to suggest that Rip Flintolocke, a character who hasn't even been seen beyond being a shadowed figure, is responsible for everything that's happened in Grymm and Creepknight's lives.