[Note: a spoiler for the game Dragon Age: Awakening follows.]
One of the design questions that developers of most computer games usually need to address is how to explain the bad guys. You generally play some kind of hero up against the forces of evil -- well, what makes them evil? Why do they oppose whatever it is you want, and how good are they at their job?
In nearly all the computer games I can think of, the choice seems to come down to "Stupid Evil" versus "Misunderstood Evil." For action games, it's almost always Stupid Evil. When Stupid Evil is personified, there's simply some generic bad guy. He doesn't need explanations; he's just eeeeeeevil. This is an offhanded justification for the existence of waves of equally stupid enemies for the player's character to cut down like wheat before a scythe.
Wolfenstein 3D and DOOM, which focused on action over story, took this approach. In a Stupid Evil game, the enemies are intended to be disposable challenges with no moral/ethical component; the point is fun through action.
Some games do try to set the action within a story, where the opposition has a reason for trying to do whatever it does. But in most cases the opposition is almost never driven by a truly malign intelligence -- it's most often painted as Misunderstood Evil, as someone who only does horrible things for nearly-plausible reasons. The darkspawn in Dragon Age: Origins were driven by Stupid Evil; they were simply monsters. In Dragon Age: Awakening we are offered an explanation for the waves of enemy beings we've been slaughtering, but it turns out to be a Misunderstood Evil, a good intention gone wrong.
Sometimes the Misunderstood Evil is even deliberately painted as being no more than an alternative lifestyle, in a moral equivalency that says everyone is equally bad. This was the direction Blizzard went when it adapted the Stupid Evil Horde of the Warcraft real-time strategy games to the massively multiplayer online format. In World of Warcraft, the Horde are depicted as ethically no more good or evil than the Alliance.
To some extent, the Imperial faction in the online game Star Wars Galaxies was given the same Misunderstood Evil treatment. Rather than letting players be consciously evil as the Empire was clearly portrayed in the films, the developers felt it was necessary to allow Imperial players to justify their evil actions as not really evil. "Sorry about that whole blowing-up-Alderaan thing, just a misunderstanding, really."
Every now and then, though, there's a "Smart Evil." This is a villain (such as GLaDOS in the game Portal) who really does hate you and who actively, intelligently and unapologetically wants to do you harm. These are the truly memorable baddies because they don't make any excuses for choosing to knowingly commit acts of evil. Like Lucifer in Paradise Lost, Smart Evil enemies are more interesting than Stupid Evil or Misunderstood Evil (and possibly even more interesting than Good) because they present a clear alternative to the Good that seems like the choice any rational being would make. We want to know *why* they choose to oppose us, why they hate us so...
...and that search for understanding is the beating heart of a great story.
Why aren't there more games that offer the challenge of Smart Evil?