The Box of Flares is a special crate that spawns near the entrance of dark levels. It contains three flares.
It serves an invaluable mobile light source if carried around; opening it (as you would open a crate) causes it to vanish and scatter the three flares, each of which release the same amount of light as the unopened box.
This allows you to spread the flares around to light up more area, although you must now juggle three flares. You may also wish to open the box in order to throw a flare down a shaft, without the risk of losing your only light source if it becomes irretrievable.
Dropping the box in water causes all the flares to be destroyed.