Villains

Benjamin D Puppet
Benjamin D Puppet is a doll that somehow represents Benjamin Daniels and it's the puppet of the media... while Benjamin Daniels is much more powerfull... or atleast, used to be much more powerfull back when he were still a sixth dimensional character... but he fucked up and is now a mortal... Benjamin D Puppet was foreshadowed to be the final boss fight in Season 1 but Teacher killed the doll... or maybe he didn't... maybe the doll was never alive... as Tentakuro has already stated in Season 1 Episode 7...

Teacher
his name has never been revealed... he is the cult leader of the L50 (or whatever their cult is called)

in Season 1 Episode 11 it is revealed that he planned the events of Season 1 by creating the red night of halloween for unknown reasons... in Season 1 Episode 13 he "killed" Benjamin D Puppet so that he can claim Jeff's book once again for unknown reasons... most of his actions are questionable and his reasons are unknown and might never be revealed as he got killed of by Tentakuro...

Makogon (EMMBC)
Kobal+Martin=Makogon... the 2 of them are not actually villains but in Season 2 Episode 4 they were roleplaying the final boss... Kobal made everyone kill each other while Martin was planning on his double-cross...

Vampirate Teacher
yes... you actually thought this guy is the good guy? no! he's the leader of a group Vampirates and they're coming... when Oliver kills Vampiate Teacher, it is time for darkness around here...

Pre-Boss???
spoilers

Final Boss???
spoilers