If your in the BayArea as you know winter equals rain here. Just get some knickers, a rain jacket (yellow, etc) and an extra layer. I have a beanie/cap I wear when its cold. If your in NorCal where it really snows then do what bikerjulio said.
With the recent weather in the East Bay I'm wearing my fall/winter gear NOW: base layer, standard jersey & bibs, arm & knee warmers, windstopper vest.
In colder weather I'll add full length gloves, shoe covers, tights, and a full windbreaker.
I am in SF and I have been going out with bike shorts, thin cycling socks, and a cotton t-shirt (i know) in the fog. Every pedestrian I see is bundled up, but if I do likewise I feel as if I am burning up.
I ride in the South Bay throughout the seasons except for when it rains. Our weather usually stays nice until around Halloween, then we still have many really nice sunny days with the mornings and evenings cooling down rapidly. Around the middle of November it really starts to cool down and that's when you need to wear layers, leg and arm warmers. The clothes that I have found work best for me are a wicking undershirt (I like the sleeveless ones), windproof/water resistant vest with mesh back (one of the most versatile pieces of clothing you can have, and works great when riding fast and keeping the cold air off the front of your body), arm warmers, leg/knee warmers, coated shoe covers (usually wear them from when temps are 50 degrees or less), wintex or coated full finger gloves, fleece cap (one that can covers your ears), a clear vinyl waterproof jacket (carry only if I think it's going to rain, and only wear it after I'm starting to get soaked - these do no breath well, so you'll sweat in these), and thermal long sleeve jersey. I also have a pair of thermal bib knickers that are nice on colder days. With a combination of these items you should be able to comfortably ride from Fall, through the Winter and into Spring when it starts warming again.
My cool weather setup for nor cal is Undershirt, bibs and jersey, knee warmers (or full leg warmers depending on how cold it is), arm warmers wind vest, bandanna (that I pull over my ears when it's real cold), cold weather gloves, and booties (only when it's real cold).
I have used this setup for many years and it works 95% of the time. I have some extreme weather stuff, but I rarely use it.
I've always found the key was warm gloves, booties and skullcap under the helmet. Don't skimp on those. When it starts raining: indoor trainer and hard intervals. Not that I'm 'scared' of riding in the rain, I just don't have time to be cleaning my bike after every ride.
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