We are from the SF Bay Area and just got back from our first trip to SD. Thanks to e.d.'s post on this board and the very good directions, we were able to go to Izakaya Sakura on 3904 Convoy, which we enjoyed immensely.
My husband is from Osaka and we are always looking for authentic Japanese food. Although most of the discussion of this restaurant on the board has been about sushi, we mainly ate the izakaya (bar) food that they offer. We had karei kara-age (fried flounder); yaki nasu (grilled eggplant); niku-jaga (beef and potato); and much more that I can't remember now! All very delicious and not something you find in every Japanese restaurant in the U.S.
All the customers were Japanese and the place had a very authentic feel. If you're looking for Japanese food in SD and not the typical "California" sushi bars that are so ubiquitous there, try and find a copy of Yuu Yuu, a free, semi-monthly Japanese newspaper. Yes, it's almost all in Japanese, but the ads for restaurants usually have enough English and photos so that you can figure out what they serve and where they are. I'm sure most of the restaurants are worth going to.