The best place to start in your journey to a warmer ride is as close to your body as possible. Having a good base layer is one of the more important aspects of keeping warm on cold rides, because it's the last layer of protection you have against the cold and biting winter winds you'll face. A base layer can be anything from basic cotton long johns to more advanced fleece underwear. You want something that'll not only keep you warm, but also will feel good against your skin as you put in the miles.
Material aside, the most important thing about your base layer is the fit. You'll want that first layer to be snug while still allowing you the freedom to change positions on the bike and walk around on your rest stops. A close-fitting base layer will actually keep your body warmer, since there is less air that can flow between the clothes and your body. Less air means that your natural body heat will be retained longer.