If you really want some good japanese food, there are a couple places I would definitely recommend:
Tani's Kitchen:
My Favorite Japanese place in the SF area. This place really isn't big on sushi, but the rest is absolutely great. I usually get the Spicy BBQ Hamburger Steak, amazingly good.
Muracci's:
This place opened up not too long ago, but IMO is the best Japanese style curry you can get in Norcal. Curry is all homemade (none of that Golden Curry boxed stuff). Park at Portsmouth Garage since its closeby and isn't all that expensive for parking ($2.50 an hour)
Genki Ramen:
I wouldn't really go here for the ramen, but if you like Okonomiyaki this is one of the only places in Norcal to get it (way better than Izumiya's in Japantown)
Ajisen Ramen:
I'd rate this #2 on my list of Ramen places in Norcal. Great Variety and decently priced.
Santa Ramen:
This place is supposed to be famous for their Tonkotsu Ramen. I thought this place was pretty enjoyable but the waitresses rush you a bit since theres always a long line.
Kahoo Ramen:
My favorite Ramen place in Norcal. Amazing Ramen and if you aren't feeling like noodles, all of their rice plates are delicious. Place always has a long line to get in, so usually takes about half an hour to get seated once you get there.
Tomi Sushi:
A friend recommended me this place and told me that he used to go here and order $100+ worth of sushi with just 2 people and he's a real sushi snob. Some of the best sushi I've ever had, though it is very very pricey.
I'm sure I'm forgetting a couple places, but these are the ones that come to mind first.