Chroma key in games is another term for 1-bit transparency.
In the film & video worlds, chromakey means to "key" to a particular color and make it transparent, like with bluescreening. In games it usually means to make a particular RGB color in a texture 100% transparent, and all other colors 100% opaque.
It's a cheap way to get transparency, since you don't need an alpha channel. However it means the transparency has a rough pixelized edge. A good color to designate for chromakey is one that you won't be using elsewhere in your textures, like magenta (1,0,1). Whatever the color you decide, all textures in the engine will use that same color for chromakey.
See also Billboard.