The basic idea in cold weather is to protect your core (your torso and chest) from the cold. Your body will limit blood flow to your extremities in order to protect your internal organs. That's why your hands, feet, legs, and arms get cold and numb...very dangerous when riding. I'll be investing in a heated vest this winter for this specific purpose; if your core is warm, the rest of your body will handle things better.
Start with a good base layer, think long thermal underwear. A balaclava to protect your face and neck. Add your normal clothing. Then a basic fleece mid-layer vest/sweater.
For a jacket, invest in something water/wind proof, with a good thermal liner and minimal venting. I bought a Merlin Hamstall jacket...it has an Outlast liner in it, great for very cold weather.
Good gloves are a must. You might want to consider heated gloves or heated grips. Again, you want water/wind proofing and zero venting. Wearing glove liners inside summer gloves will NOT do the trick. Be careful not to buy gloves that are overly thick as it can impede tactile controls on levers and whatnot. My suggestion is to shop around and try gloves on, the right gloves will be different for everyone, so find the ones that meet your needs. I do suggest finding a glove with a gauntlet, to aide in keeping the elements from creeping into your jacket.
I have Highway 21 RPM boots, great basic motorcycle boot with water proofing at a reasonable price. Good wool socks are a must and are generally very comfortable to wear with any boot. If you're wearing basic shoes in the winter, then you're a glutton for punishment. And god forbid you ever go down...you want quality boots on your feet.
Outside of that, make sure to give your bike some time to warm up before riding. Let it idle for at least 5 minutes. Make sure your levers and brakes are free and not stiff from the cold. And cold tires are dangerous tires, so take it slow and easy. Also, make it a habit to check your tire pressure all the **** time. Ride safe...