I'm surprised nobody has mentioned e-bikes. As far as I can tell, that is the answer to the bay area traffic. Since I bought one roughly 5 months ago, I've commuted almost 3000 miles. My commute is the same every day, and it is a lot faster than a bad day of traffic. The bonus is that I don't have to change into bike clothes or shower.
Details:
12 mile commute
40 minutes by ebike, every day
25 minutes by car, best day
50 minutes by car, average day
1 hour 40 minutes by car, average day