This is my fourth winter commuting by bike.
On top, I do a synthetic "wicking" base layer, a Chrome merino wool zip hoodie, a Sierra Designs fleece zip jacket and then an Arc'teryx softshell jacket. I'm happy with this setup because it's warm without being too bulky.
I always wear a base layer under my jeans, and when it's below 30, I wear a ski mask under my hat.
I wear glove liners under a fairly stout pair of ski gloves, and wool socks under my Specialized "Defroster" MTB winter riding shoes, but I still struggle with cold toes and fingers. I've even tried those heat packs in my shoes and gloves with no success.
The only sure fire way I've found to stay warm is to ride fast (like I'm on a training ride). If I take a leisurely ride, I pay for it with painful digits. Riding on the Lakefront (instead of in traffic) helps me keep my speed and body heat up.
Regarding my winter bike, I switch to my single speed mountain bike the first time it snows and ride it until the spring. I've found I can safely ride my mountain bike in deep snow and on ice, whereas I don't feel particularly safe in snow on a road bike. Since bike maintenance is a bitch during the winter, I avoid riding my other bikes...especially my geared road bike. I don't try hard to keep my winter bike bike clean, but I'm trying to clean and lube the drivetrain at least once per week.
Currently I'm looking for a way to protect my eyes when riding during a snowstorm. Glasses fog up. But with no glasses, snow feels like needles. Also, my eyelashes freeze together, welding my eyelids shut. Will ski goggles do the trick? Any other suggestions?