The Castelli Pioggia waterproof booties are ideal for protecting your feet from the rain, provided it's not too cold.
They're made of a thin polyurethane-coated waterproof fabric and feature a strip of silicone rubber at the ankle, which stops water running down your leg and into your shoes. The combination works very well, and they kept my shoes dry during downpours, intermittent showers and long rides on wet roads.
Being thin means that they're not really suitable when it's wet and below about 10ºC. This doesn't make them ideal for cold northern hemisphere winters, but they will get plenty of use throughout the rest of the year, without overheating your feet.
The other problem with being thin is that the bases are prone to small holes and tears. You have to be extra careful about where you walk while wearing them.
The Pioggias are available in five sizes (S to 2XL) and come in black with reflective trim. Finally, they're not cheap at £45 a pair.