Flares are used by either holding them in Alan's hand or by throwing them down. Alan can use flares to keep the darkness away as well as to burn the darkness away from the Taken. When he sets off a flare, the Taken try to move away from it. Whilst it won't kill the Taken directly, it will burn away the darkness fully if close enough.
The Flare gun is the most powerful unconventional weapon in the game. It fires slowly, but deals tremendous damage over large areas. It is capable of killing multiple taken in one shot and even kills larger Taken with ease. Ammo is extremely rare.
Flashbang grenades are police grade weapons that can be used. They act like normal grenades against Taken, because of the violent flash. They are rare early on, but eventually they become readily available. They cannot be used at the same time as flares.