Stare too long into the abyss and the abyss stares back.Friedrich Nietzsche
Darkness is usually the symbol of evil. Often, it is classified as a type of energy that the villain draws upon. In many good vs. evil stories, light is the good, the antithesis of the negative darkness.
Examples of Darkness as a symbol of evil comes from the fact it is used in many villains' names, the "Prince of Darkness" (sometimes called "King of Darkness") is also a fairly common alternative name for The Devil himself - also in many fantasy settings the word "Dark" is suggestive of an evil-version of a species of faction that is normal good (or even a more malignant type of an already evil species/faction) - examples of this are the Dark Elves (from Scandinavian mythology into later many different settings) and Dark Eldar (from Warhammer 40K).
In many religions and philosophies, darkness is seen as one of the most ancient forces, predating almost all things and in many ways, being related to the Greek concept of chaos (an empty void that existed before the "ordered" universe) - this darkness is not always seen as evil but it can be seen as negative, especially in the fact it represents either an absence of life or order - both of which are seen by many as unwanted states of existence.
On a related note, darkness can be harnessed for good just as light can be abused for selfish or sinister purposes. In the hands of heroes and other good guys who know how to properly harness it, the element typically assumes "pure" state thus emphasizes its beneficial aspects to counter villains' "tainted" state that leaned to its harmful ones. The philosophical interpretation behind it is acknowledged that light and darkness can and must exist only simultaneously. Even a dark god who morally grey at best had necessary role to ensure that the balance remains undisturbed. If anything, light alone is not always enough to overcome evil, but the balanced combination between it and darkness is.
Darkness can also be represented as a sentient - or at the least intelligent - force in itself, whenever this is applied it is almost always evil. Examples of darkness being seen as sentient or somehow "alive" can be seen in the certain villain types such as the Dark Form or Dark Lord, depending on the writer.
Darkness is also used to classify a work of fiction as containing mature and often depressing and/or disturbing content such as death and suffering - it can also be used to refer to a personality-type that is prone to more negative thoughts or actions, such as a fixation on death or suffering: some subcultures (especially Goths and Emos) deliberately idolize this personality-type and may dress in black and listen to music that deals with angst or death as part of their identity.