I went to Payless Shoesource and got some $25 "waterproof" hiking boots. Heavy, yes. The do work to an acceptable degree, but they are not really waterproof. When I get to work, my socks usually are wet at the places that would be under the seams of the boots. I have tried a couple things to seal up the seams, and nothing has been perfect.
My solution is adequate, but one of the tools I use to keep my motivation up is the search for the perfect commuting gear, so I still am looking for a better solution. I am considering getting a pair of those high rubber boots and then cutting them down to about six inches. I have sewn extensions to the legs of my rain pants so that they overlap the tops of any footwear I might use, so I'm thinking that rubber boots combined with the long rain pants will be the ultimate in dry feet. The high rubber boots would be hard to ride in (I have tried it) but I am hoping that shorter rubber boots would be OK.
I keep a pair of regular shoes under my desk at work, so looking normal at work is a problem that has been solved.