Unfortunately, the choices aren't great. I've actually done this once before, and am not sure I'd do it again. There is the Commuter Shuttle Bus that runs from various places in El Dorado County to the Amtrak Train station in Sacramento. Or you can take the city train system from Folsom to the Amtrak Train station in Sac. From there, you take an Amtrak train to Emeryville (or you can get off at a BART station along the way). In Emeryville they'll shuttle you over on a bus to SF.
These options take a while, and were the best I could find at the time.
Anyone else have other suggestions?