You should not use normal stain on top of a polyurethane finish. However, some polyurethane-blend stains are designed to be used over a polyurethane finish.
If you want to touch up furniture with a polyurethane finish without completely refinishing the piece, you can use a polyurethane stain blend like those sold on Minwax.com. This is exactly what it sounds like: polyurethane blended with stain so that you can apply it over a polyurethane finish. A second option is to use oil-based paint, but these types of paints can mask the natural wood grain. When applying any kind of stain, windows should be kept open for ventilation.