Wakuriya and Mitsunobu are modern California/hybrid kaiseki style restaurants, the most high end that I can think of. The only thing about Mitsunobu from Yelp pics I've seen is that the portions might not be sufficient, and you are paying $$$ for real estate as well.
Kappou Goumi in SF on Geary is less formal but you can get some very nice kappo style dining...in California many people misunderstand the concept of Kappo vs kaiseki. The equivalent of Kappou Goumi in SF would be Hachi Ju Hachi in Saratoga. HJH's menu as seen from some Yelp pictures, looks more like the typical izakaya you find in Taipei, where they properly categorize items by cooking style (yakimono, agemono, nabemono)....the nabemono selection is modest but looks to be something great to have during winter. Kappo Nami Nami is a decent choice in downtown Mountain View, with a more modern decor and vibe.
The other place in SF can be quite decent...Kappa in SF J-town...ko-ryori (people confuse it with kaiseki).
Jin Sho in Palo Alto is a Nobu (NY) spinoff, but Kaneko-san there was formally trained in kaiseki, and really knows how to make a killer dashi (and can come up with off menu stuff). If you want something more traditional (than fusion) just sit at the counter and speak with the owners. Steve Jobs may have loved this place, but I think Steve being primarily vegetarian, enjoyed other things rather than something like anago with kimo-sui (fresh eel liver in dashi) or isaki or kawahagi. Jin Sho's nigiri is also excellent. Probably on par with Sakae in Burlingame.
For something more casual, Ippuku in Berkeley it is said, has the best most authentic yakitori, but you have to insist on Japanese style cooking of the chicken (ask for it seared/rare on the inside vs fully cooked). For lunch they appear to have imported buckwheat flour from Hokkaido to make their own soba. But definitely do yakitori for dinner. In the South Bay, Sumika is king (for yakitori) but only if executive chef Maru-chan is working in house the night you go, and check out their website for some seasonal specials. Last August/June they imported ayu (sweet fish) and it was done shioyaki over their binchotan (imported Japanese charcoal) and it was just absolutely stunning. The $17++ Japanese sanma shioyaki was a bit too expensive for my liking but I'm sure it was good, and the matsutake dobinmushi was excellent too last year. For a non yakitori themed izakaya, Hoshi in Santa Clara is your best bet (they even have kusaya and many other rarely seen items/dishes, and 3 course fugu during winter).
Dan Izakaya (San Jose) specializes in horumonyaki, but not sure how that is.
There's also Sakae Sushi in Burlingame.
For less formal / more casual eats:
Yu-Raku (San Mateo) - chuka ryori (Japanese style Chinese).
Usagi (San Mateo) - yoshoku (the best one we have, I'm sure easily beats On The Bridge in SF Jtown which is not even that good)
Gyu-Kaku (Cupertino) - Japanese BBQ/yakiniku, a chain wtih locations in JP, Los Angeles, our only NorCal location
I wouldn't bother with ramen at all.
But like you said in the SF sushi thread, we're still leagues behind LA and NY Japanese, but at least it's better than it was 10++ years ago.
Already mentioned are good ideas - here's a couple more -
1. Jin Sho in Palo Alto was beloved by Steve Jobs, Japanese people love name brand like that.
2. Sumika in Los Altos is a very authentic Yakitori experience
3. You should just take them to Alexander's for an american steakhouse - with Kobe beef!
4. Kapo Nami Nami in mountain view deserves more traffic. It's good, and fairly impressive without being over the top. Also kaiseki style, with good chinmi. The chefs don't speak much english.
That's a big geographical area....could you narrow it a bit?
1. Are you sure they're going to want Japanese?? Japanese food in this area is not as good as Japanese food in Japan.
2. Akane has good sushi,slightly casual for a client dinner depending on the client. Jin Sho is a little more formal, but the sushi can be a little uneven.
For a long time Fuki Sushi was the mainstay for client dinners, but it edged on a bad meal the last time I was there.