I fun prank used to be setting someone's color scheme to black on black with black highlights. It didn't work as well on later versions of windows because the button highlights were always visible. In 3.1 you'd have to guess where the buttons even were.
Win3.x and 9x are based on DOS, so all you need to do is boot to a DOS prompt and edit CONTROL.INI (a text file) to change the colour scheme or its colours.
