Arguably the ultimate Hellboy villain in the sense of being the greatest threat he ever faced, the battle with The Queen of Blood is the point that the final trilogy of Darkness Calls, The Wild Hunt, and The Storm and the Fury, the finest Hellboy stories of all, were building up to. The Hellboy universe's version of Nimue, the Arthurian enchantress who seduced and then trapped Merlin, The Queen of Blood is a witch of such unimaginable darkness and power that all the other witches are terrified of her. It's always a satisfying introduction to a major villain to show how their excesses are such that even the usual villains are disturbed at what they could do. In this case this is very apparent by how centuries ago the other witches killed her and chopped her body into pieces scattered across the world and, when the pieces kept bringing themselves back together, locked them in a chest and buried it deep within the earth with a giant to guard it. Fortunately, the character lives up to this build up, becoming a dragon embodied with the apocalyptic power of the Ogdru Jahad. The Queen of Blood story brings about destruction on an enormous and almost unstoppable scale. There's a reason, after all, that the next installment is called Hellboy in Hell!
6. Johann Kraus
When Hellboy and the BPRD went their separate ways and Mignola decided to turn BPRD into a spin-off with 2002's Hollow Earth arc, there was a need to create a greater cast of weird enhanced agents to flesh out the Bureau's team. Comfortably the best of these new additions was German ectoplasmic medium in a rubber suit Johann Kraus. His body having been destroyed by a huge shockwave of psychic energy while he was conducting a seance, Johann is left as a spirit without a home - not dead, just bodyless. It's his desire for a new physical form that drives a lot of Johann's storylines. Unlike some of the other supernatural heroes in the series who are brooding and troubled, Johann's strength as a character is that, for all that he looks bizarre, he is friendly, ingratiating and well liked, equally happy working with research and records as he is in the field. Recently, though, his obsession with gaining a real flesh and blood body has begun to take over. It's possible that over time we could start to see a darker version of the affable teutonic ghost.