When running a game your players are going to require an antogonist. More often than not they are going to be playing "good guys"; characters who have morals, ethics, just causes, a desire to keep the loss of life and property damage to a minimum.
All right, the last is probably not the case because frankly blowing shit up is fun whether you are a good guy or a bad guy.
So in creating your antagonists you are going to need to give it considerable thought. They are NPCs, but among the most important of NPCs. They will be driving the plot of your game, giving your PCs motivation and reason for existing. So, what makes a good bad guy?
Motivation. What does he/she want? Power? Wealth? As Alfred in The Dark Knight said, "To watch the world burn"? Is it just to make the heroes' lives miserable? A clear cut motivation is important to give a villain dimension, this is as true in a role playing game as it is in a novel. The Emperor in Star Wars wanted to control everything, Batman's Riddler does it for greed and cheap thrills. The Green Goblin is motivated by as much greed as he is a desire to make Spider Man's life a living hell. Establish your villains' goals and desires, stay true to them. Or if they change, give a good reason. Perhaps greed was their initial motivation but they were humiliated by the heroes. Now their focus, their reason for living has changed.
And not all motivations need to necessarily run contrary to the heroes'. In my Vindicators game I have a character called Doctor Hades. Hades' body was blown up by Photon (an accident) and now the doctor's consciousness lives on as an artificial intelligence. Through role playing the relationship between hero and villain has become complex as in a potential future Photon becomes a villain, Hades his minion. It has been fun determining if indeed this future pans out and my player seems to have a great deal of fun every time his character and Hades cross paths.
This is not the only instance where a villain may reform or at least cease to become an enemy. DC's Catwoman is a prime example of this. In Marvel Wolverine was enemies with The Silver Samurai but their rivalry evolved over time. The X-Men's Magneto under Chris Claremont's tenure on that comic had a tremendous evolution.
Methods. How do your villains operate? Do they work alone or do they have legions of faceless minions? Again, consistency is key here. If a bad guy operated alone in the first adventure and then suddenly shows up with an army of thugs in the second, you need to have a good reason. Perhaps the army is part of a mystery,
or perhaps the bad guy talks about how he has "learned his lesson from the last encounter". You need to be prepared to explain it. If a villain employed hi-tech devices and is not a master of sorcery again you had been have a good reason for the sudden change in modus operandi.
How ruthless is too ruthless? IO9 had a fantastic article regarding this. In various genres heroes are left helpless or the villain has some opportunity to kill them, and they choose not to for one seemingly moronic reason or another. Not all villains are murderous, true, but those that are had better have a good reason not to be. In my super hero universe it is implied that if the villains get too psychotic then that would result in an escalation. If too many heroes wind up dead or critically wounded, if their loved ones are targeted, then the gloves are off. There are NPC heroes that would certainly have no qualms about hard core retaliation.
But that does not mean I have made the game safe for heroes, far from it. Early on I noticed that whenever a PC was stunned or knocked unconscious, no one bothered to protect them. Fellow players would let their team mates lay where they fell regardless of the possibility their unconscious/helpless forms could be used
as hostages or living shields. I mentioned this on more than one ocassion and it generally went unheeded; players were having too much fun fighting to do simple things like protect their own. So in one adventure a hero was knocked unconscious, no one went to help even though a couple of them could have come to his aid.
And so one of the bad guys shot the unconscious hero in the head, killing him.
It was not a popular decision.
The fallout was I eventually lost both players and it was not until years later that one of them came back (the guy who ran the dead PC and I have spoken since and he is okay with it, but we never gamed again). Could I have handled it differently? Yes, absolutely. Paragon should have been used as a human shield, he should have been kidnapped and held for ransom. The costume that provided the source of his powers should have been taken from him and an adventure could have been made surrounding it's retrieval. I lost two players and screwed up, all because I wanted to make a point.
Here is what I should have done. Walk away for a few days. Calm down, assess the situation, regard the consequences. I should have contacted Paragon's player and asked him how he would feel if his character were killed. It was a knee-jerk reaction and those never work out.
Does this mean I think death should be taken off the table entirely? Certainly not. If players are making stupid decisions then there should be consequences, and sometimes (very rarely) death is one of them. Perhaps death is too harsh and a simple trip to the hospital is all that is needed?
So to sum up, villains should be fully fleshed out characters with consistent motivations, or their inconsistencies should either be explained, or discovering their reason for being be made part of the adventure. Villains with a capacity for murder and do not should have a valid reason for not going hardcore, and if you have an urge to kill your players' characters, walk away from the game for a while and seriously consider your actions.