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Most ramen places in San Francisco are run by Chinese or Korean.  If you want something authentic, you need to head south a little.

Santouka in San Jose is on the top of my list, but it's more of a shop in a food court rather than a restaurant and their portions are very small.  I also like Orenchi in Santa Clara, but beware they are only open for a few hours a day.  Santa Ramen in San Mateo is too greasy for me, but good flavor nonetheless.  You should try them all and see which one you like.