I paid $40 for a pair of BBB Hardware shoe covers, made from neoprene. They added a good layer of wind/waterproofing and let me wear my SPD sandals until late fall -- then I went right into heavy boots.

If you go this route, you should buy a pair 2-3 sizes bigger than your shoe size. Also, watch the crank arms. I tore my left overshoe because it was rubbing slightly.