Amtrak (www.amtrak.com [1]) trains run several corridors through the state. The California Zephyr, Capitol Corridor, Coast Starlight, and San Joaquins routes offer services to Auburn, Sacramento, Emeryville, Oakland [2], San Jose [3], Los Angeles [4], the Central Coast [5], and the Central Valley. Train are roomy, comfortable, and offer a dining car for affordable snacks and meals.
Links:
[1] http://www.amtrak.com
[2] http://www.moon.com/destinations/california/san-francisco-and-the-bay-area/east-bay/oakland-and-alameda
[3] http://www.moon.com/destinations/california/san-francisco-and-the-bay-area/silicon-valley/san-jose
[4] http://www.moon.com/destinations/california/los-angeles-and-orange-county
[5] http://www.moon.com/destinations/california/central-coast