The concept of duality is basically that of two opposing forces that are ever in conflict. This conflict never has a clear cut winner and continues on indefinitely. Duality can also be present as a middle path, when the characters focus on never taking aside and rather taking what's best from both sides of the conflict in order to achieve the completeness of one's self. Duality may also be present as a gameplay mechanic, by having two different sets of colors or objects that are to be used either complementary with each other or be used to negate one another. And sometimes duality is used in a completely complementary sense, when something cannot exist without the other, like the mind and body.
Good VS. Evil
The concept of duality in good vs. evil is present in many games. However it can only be considered a duality concept when the conflict is depicted as everlasting and never having any true resolution. For example the endless battle between the different Links and Ganon, or the endless conflict between Heaven and Hell in the Diablo series. As well as the conflict between the light warriors and the Dark warriors depicted in Final Fantasy IV.
As a Western RPG mechanic
The duality of Good and Evil has also been incorporated as a game mechanic in different RPGs, Knights of the Old republic, Oblivion, Fallout, and Fable all adhere to a system in which good deeds, give a karmic bonus which is incorporated into your character making NPCs react to you differently or offer you different quests, same with doing different evil deeds.
Fate VS. Free Will
In Final Fantasy XII the players have the opportunity to take fate from the Gods' hands and restore back into humanity. A similar conflict is seen with Kratos in the God of War series. This type of conflict personifies the ever haunting question: Do we have free will or are all the events in our lives predetermined by Fate?
Light VS. Darkness
Light and Dark are used quite often as gameplay elements. In many games Light and Dark are used to symbolize good and evil. In all of the Star Wars games Light and Dark are used to represent the two sides of the force, with the Jedi exemplifying altruism and light, against the Sith personifying selfishness and darkness. Throughout the story both sides constantly struggle and lose, sometimes the Sith almost completely wipe out the Jedi, other times the Jedi nearly annihilate the Sith. The conflict is brought to a resolution by Luke Skywalker's desire to balance both sides. Light and Darkness can also be used in mirror reflections.
Light and Darkness are also present as Parallel Worlds, or dual existences. As seen in both the Twilight Princess, and a Link to the Past. Hyrule has two existences, one light and one dark, that mirror each other in similar ways (although not perfectly) and the player must traverse both of them.
Fire and Ice
Fire melts Ice and Ice douses fire. A gameplay mechanic that has been present in many puzzle solving and platforming games. Exemplified by the enemy Twinrova in Ocarina of Time.
Elemental magic is present in many different games, most notably RPGs, and has clear examples in the Final Fantasy series. Elemetal Magic may include: fire, ice, thunder, dark, light, earth, air, water. The concept of dualtiy comes into play as a gameplay mechanic enemies of fire are weak against ice and vice versa. Many RPGs have adopted this formula for their magic and it has become a rule of the genre.
Mind and Body
The importance of Mind and Body are critical to certain games. In Kingdom Hearts, the characters struggle with the darkness within themselves as well as the possibility of losing their hearts, which would corrupt their bodies.
Color based duality
Sometimes in puzzle games switches come in two different colors, using a certain colored switch takes down a certain colored barrier while bringing up the previous one. This is notable in a Link to the Past, with the color switching orbs in certain dungeons.
Parrallel worlds in mirrors, reflections and evil twins also are counted as part of the duality which exists between these double objects. In the Kingdom Hearts series Duality is present amongst the Heartless and those without Hearts. Later a third party comes into play in the conflict, the Nobodies, which upset the dual balance and have the other two work together to eradicate them.
Nature and Technology
Nature and Technology are also an important duality concept. This is represented in Final fantasy VII where technology is seen as taking away the life force of the planet and consuming the forests and the rivers. Basically any game that touches on the destruction of nature to advance the human race.
Japanese Shoot Em Ups
In many Japanese shoot em ups the concept of duality is used in a color based gameplay. The player may switch whenever he wants between two colors. When the player is one color he is immune to all the bullets of that same color and he can destroy enemies with an opposite color.