John Doe was shown quite clearly in the film, played by Kevin Spacey. The interesting thing about Doe is that he thinks he's doing a good thing by creating this amazing piece of performance art that point out our sinful side. In fact, he even talks about how he's doing society a favour by offing his 'victims'.

Those are my favourite bad guys: the ones that don't know they're bad guys. One of the two villians in 'Mission Impossible: 3' carefully explains to the Tom Cruise character how America will benefit by middle-eastern terrorists getting a super powerful bio-weapon (the film's McGuffin). In his mind it makes sense, and will eventually end up being good for everyone.

You find these types of bad guys in fiction (Magneto from 'X-Men') and reality (Hitler, Bin Laden). They are absolutely convinced they're making the world a better place. Actors who play bad-guy roles keep an old saying in mind when trying to find motivation for their character: "the villian is the hero of his own story".