they could do this by adding in some sort of stereoglyphic design in the game itself, whether in the texture rendering or whatnot. you don't notice the stereoglyph inside the game with the 3D turned off, but as soon as you turn it on, voila, the stereoglyph becomes visible as its parts converge.
it'll be pretty hard to effectively employ this though, but a good proof of concept would be a 2D picture with a stereoglyph hidden in it. well, hidden, or disabled, until you enable 3D.
EDIT: stereoglyph==stereograms (correct term)
and i just thought of a good way to employ this with movement. the stereogram would have to be rendered in real-time, and on 2D you'd only catch it as sort of a moving pixellation, something like a mirage (it should slightly distort whatever textures are behind it). that'd make you suspicious, as you see movement but you can't quite focus on it. so turn the 3D on, and the stereogram pops out as the distortion converges into something more clearly defined... like a ghost, for example.