See list of Qualities.
The dark quality is where not everything is quite right. For example the conspiracy of those in power in the X-files gives it a dark quality. This seems to be the current vogue in role-playing games and personally I hate it, but only because its done badly. For example while wolf's World Of Darkness has as a key theme the self disgust of characters, and the knowledge that eventually immortality will cause you to spiral down into depravity. In addition it has a Machiavellian flavour of intrigue and corruption. Its good fun to play in, except that I've only ever met three GM's that could actually run it well. Cyberpunk can be dark, although systems like Shadowrun tend to stifle the style and encourage light playing.
The problem is that a good dark game is a careful balance of hope and despair. If you character is plummeting into despair, the GM should let them see the light at the end of the tunnel, if they start relying on aid from somebody, it should get cut off, characters, and indeed players, in dark games should always be on the edge, not trusting any but the closest of friendships forged with care. Look at the X-files and you'll see all these points.
Earlier I mentioned three GM's who could run World Of Darkness, well I know fifteen who think they can, and can't. The trouble is some people who think that they are being smart with plot and counter plot get more intrigued in the plots and give less time for character development and recovery, these people sink into the extra-dark style of play.