No recs for dinner, but I always love The Lighthouse in Sausalito (also in San Rafael) for lunch/breakfast. No-frills, but popular with locals, and menu includes some Danish specialties. The mixed fruit pancakes are a must for breakfast.
Buckeye is a good rec. Lark Creek Inn is WAY overpriced, IMHO.
There is only one "have to do" resto in the area, Sushi Ran in Sausalito. Along with Hana in Rohnert Park, best sushi in the North Bay.
Poggio and Fish are two places in Sausalito I haven't been to that get good pub.
San Rafael has better dining options than Sausalito, but they are more "everyday" places, and you won't get the view or the refinement. That being said, Casa Manana or Las Camelias for Mexican. Lotus for Indian (very very good, and they have a cool retractable roof). Royal Thai. There is a wine bar called Sabor that I haven't been too, but seems very popular. Sol Food is a little Peruvian (?) place that is cheap and tasty, usually very lively. I've heard good things about Vin Antico (Italian).
Not too far away are Cucina and Insalata's in San Anselmo, and my personal favorite Picco in Larkspur.
I second many of chum lee's recommendations. Cucina and Insalata's are both delicious for Italian/Mediteranean food. I really like Lark Creek Inn, though. They've got a really good locally sourced menu, are very inventive with their dishes, have friendly service, and around 95% of their ingredients are organic.
4th St in central San Rafael has many options some that chum lee has mentioned. Sol Food is a really good unique Puerto Rican restaurant. Just look for the big green building.
I'd check out tiburon too if I were you. 3 Degrees at the Tiburon Lodge is very good and reasonably priced. There is also a tasty Japanese restaurant down by the water.
If you decide to head out to Stinson Beach, be sure to try the Parkside, they have a restaurant and a little snackbar. Their restaurant is very very good and specialize in local food. Lots of good fish, great higher end burgers, wild mushrooms when in season, etc.
I haven't been there in a while, but the Spinnaker in Sausalito is a nice place for a view and some seafood. You're literally sitting out over the water.
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