I love Sakana on Post and Taylor but it isn't flashy. Generally has real Japanese people eating there. They always have lots of interesting fish and pretty good apps.
Also, I like Ryoko's right next store. Cool atmosphere and great karaage (Japanese fried chicken) and also has other great izikaya style food (Japanese bar food).
Ryoko Restaurant & Bar
619 Taylor St, San Francisco, CA 94102
605 Post St, San Francisco, CA 94109