Bing Crosby's, Walnut Creek is excellent, though pricey. Great bar, not really for kids, but very good for adults. Around town the Left Bank chain is consistently good and more reasonable as is Max's Opera Cafe and if you get to San Jose's Santana Row Thea is wonderful.
We've always liked the Stinking Rose on Columbus in downtown SF for it's not-understated use of garlic. Motto there is "we flavor our garlic with food!"
San Francisco's restaurant scene changes almost daily but you can be assured of excellent choices everywhere. Check out the Zagat Guide to the area for more recommendations and let us know what you discover.
I second The Stinking Rose! Also, I noticed that the restaurants on Columbus are really busy late at night. (I walked by around 10pm and there were lines out the door at some restaurants!) I rushed to eat at The Stinking Rose around 6pm and there almost wasn't anyone there haha.
Osha had some of the best Thai food I've ever had in my life. It's a trendy Thai chain all over the city. I went to the one on 2nd St.