haven't been to many eateries here but there are other interesting sights:
-daiso (22 peace plaza) the variety gozilla of japan, almost everything is 1.50 here. good place to get souvenirs rather than at tourist places
-benkyodo co. 1747 buchanan, sells mochi (2ish), japanese pastry made with sweet rice flour and either fruitty or nut themed fillings.
-new people. 1746 post st. in the cafe, there's organic sausages and onigilly, japanese rice balls (2.75)
Do some searches for places in Japantown proper. Note that O Izakaya Lounge had a change in chef in 2009, so treat older reviews with caution.
There are a handful of good and affordable places along Fillmore. Delfina Pizza on California @ Fillmore is loud and crowded but is excellent, and is a good representation of what's currently popular in SF. Afterwards, if it's before 9PM on a weekday, or 10PM on Fri/Sat, you can get a dessert crepe at Sophie's Crepes in Japantown.
3621 18th St, San Francisco, CA 94110
1581 Webster St # 275, San Francisco, CA
O Izakaya Lounge
1625 Post Street, San Francisco, CA 94115
The best Japanese food isn't necessarily in Japantown, if that's what you are looking for.
I love sushi, but if I had only one night in Japantown, I would probably walk a few blocks up Fillmore to Fresca (at 2114) for Peruvian food.
2114 Fillmore St, San Francisco, CA 94115