If it's not too cold out, I tie a handkerchief around my head. First, I fold it into a triangle, then put the big point in the back and tie it like Tupac in front of my forehead. This way, I can easily remove it by pulling on the back of the bandana while cycling. Alternatively, I have an Under Armour skull cap that I can put on and pull over my ears. I push it up over my ears when I heat up. If it's really cold, I have a pasamontañas which is basically a ski mask with only one cycloptic hole for the eyes. It goes down over my neck too.
I also use a handkerchief to tie around my neck. Way better than a scarf. Once again, tie it only loosely so you can remove it once you warm up.
For the upper body, a moisture wicking shirt is the preferred base layer. I either use a long sleeve wicking shirt or a short sleeve one with arm warmers (which can be taken off).
Ideally, on top of the shirt, you will wear a zippered jacket made of polar fleece, covered by a zippered windbreaker. Fleece does not break the wind. This allows you to control your body temperature by adjusting the zipper levels of both jackets.
Cold weather is not the time to go commando. I recommend boxer-briefs or briefs with boxers on top of them. Pants too. No shorts.
As for the feet, a good moisture wicking sock is a great base layer. I've been putting baseball socks (or soccer socks, but they don't work as well since they fall down easier without shin guards) on top of those. When it's really cold, I put another fairly tall sock on the outside. Boots are a must. They keep the wind from ripping straight through your footwear.
I think this is a nearly ideal setup for me. You might find that you need to tweak it a little bit to fit your needs. I also realize that I look even less stylish than usual in this sort of get-up. You may be able to change into better looking clothes when you arrive at your destination. I just stopped caring.
Best of luck.