I use a pannier from Arkel. It came with the optional rain cover. It is bright yellow and has a wide reflective stripe. So far it has proven to be waterproof. You can order the rain covers on their own
here. If you scroll down the page under "Urban Series" you will find the "Bug Backpack Rain Cover." I imagine it would work for virtually any backpack, plus it's only $20 USD. Not bad for visibility and protection from the elements.