Down in the Peninsula Lunch topic, Melanie suggested a topic be started on favorite Chowhound Japanese restaurants in San Mateo, of which there seem to be an abundance. I'll list mine -- please let us know about yours!
Den - 30 South B Street - An authentic Japanese pub that I believe is part of a chain out of Osaka. Lots of small plates, unusual salads, snacks, sushi, etc. some of which you won't find anywhere else.
Hotaru - 33 East 3rd Ave (near El Camino) - Has a good, varied menu. My Japanese husband likes the curry dishes and the koroke (croquettes) -- you don't see these dishes at every Japanese restaurant. There's a large small plate (tsumami) menu at dinner; I especially like the teba saki (salted/grilled chicken wings). Sushi is good too.
Santa - 805 South B Street - Hands down the best ramen in the Bay Area, in my humble opinion. Tastes just like in Japan. Ramen is a noodle soup, different from soba or udon; it's the Japanese version of Chinese noodles, although I have never had any noodles that resemble ramen in a Chinese restaurant. :-)
Tombo - 212 2nd Ave. (near Ellsworth) - We've talked a lot about this place on Chowhounds. The best udon in the Bay Area. Also serves a good zosui (porridge) that isn't easy to find. Also has good sushi/sashimi. The udon suki is fantastic but you have to order 24 hours ahead.
Suzuyou - 505 2nd Ave. (near Delaware) - A kind of divey place run by an older Japanese couple on the other side of the railroad tracks. Good mizutaki and funky atmosphere. Lots of Japanese magazines to read. You'll feel like you're on some roadside place in Japan.
Brasserie Tomo - 140 W. 25th Avenue - An unusual French/Japanese fusion place with just a few tables and a counter. The menu is in Japanese only and the food is exquisite, expensive, and, unfortunately, rather small portions. The chef will do omakase, but watch your pocketbook! Good sake selection too. They sell take-out food during the day in the front of the restaurant.
Laku Ni - 325 E. 4th Ave. - Should actually be called Raku Ni (Japanese sometimes get their L's and R's mixed up). I believe Chowhounds had a dinner here awhile ago. Great home cooking counter place with only about a dozen seats. The type of place a Japanese salaryman would go to after a late night at work.