One of the best options for Japanese in SF is Kyo-ya. The place is expensive, but it continues to be one of the standard bearers for Japanese food in SF. It's extremely consistent, and you always know you'll be getting top notch ingredients - stuff like fresh wasabi and some of the best toro in town. They're also one of the few places in town that will do a kaiseki dinner, although I haven't tried one there. Here is a lunch I had recently with my dad.
toro nigiri - $20
As you can see, this toro is really, really good. It's so good you could call it the real thing with a straight face. But at $10 a pop, it's pretty prohibitive to eat too much of this stuff. As my dad says, at least it's cheaper than the real real thing in Japan...
chirashi - $32
Again, at $32 this makes for one of the more expensive chirashis around. But you do get what you pay for - 4 nice, thick slices each of maguro and hamachi, a big juicy scallop, some very fresh ika, some akagai, a piece of ebi, some kazunoku (the yellow herring roe), and some tamago. They also give you a healthy dose of ikura, though I'm not a big fan of the stuff. This thing was too big for me to finish, and all of the fish was great.
It may be expensive but at least you know what you're getting at Kyo-ya. It's good food at a high price. Now, I'm off to Marseilles to try real bouillabaisse! :)