This is one I haven't really solved yet. I take dry socks--and an entire change of dry clothes--with me. I keep an extra pair of shoes at work. Wool helps but once my shoes get soaked it doesn't matter. And I try not to bike in cold rain, if I can help it. Usually I am able to adjust my schedule to accommodate the rain. I can go in a bit earlier before the rain starts, or wait until the downpour lets up and the rain is lighter. Around here that is typically less than an hour, sometimes only a few minutes.
2009 Trek 7.2FX WSD, brooks Champion Flyer S, commuter bike