My personal favorite, as of yet, is Tsunami Sushi on Castro Street in Mountain View (although there is a place in Japantown in SF that I prefer. The name escapes me and may very well be a Japanese word that I don't know).
Anyway, Tsunami has a great selection of nigiri sushi including shellfish as well as the standards, and some unique options like saltwater eel (Anago, I believe). But their eel is the best menu item by far.
However, I am still looking for the best salmon sashimi in the Bay Area and am open to any and all suggestions...