assuming strictly limited to Sonoma/Napa and not SF/Bay Area here are some lesser known
in no particular order as they occurred to me:
1) Geyserville Grill. This was recently redone and I know the chef. Sort of off the beaten path and relatively inexpensive. Pretty simple and understated but Great food.
2) Gott's Roadside St Helena. This is right on the main drag across Napa valley (29). Used to be called Taylor's Refresher. Still the best burgers around IMHO. Inexpensive
3) Almost hate to say it but some of the best food in Sonoma County is at the Graton Casino in Rohnert Park. Not your "wine country" experience but great food in both the food court options and in the sit down restaurants. This is now the largest casino in California and it is in a multi year plan for expansion with a full resort in the works.
4) It has been a while since I had a meal at a winery but have had some great meals. Some of them have full time restaurant/meal service and others only for special events. Personally I prefer Sonoma County as it is less commercialized wrt wineries. But in Healdsburg it is pretty much Napa county Light if you like the designer label type stuff and want to find it in Sonoma county.
5) Sea Thai Bistro in Santa Rosa. Always good food.
6) El Coqui. Santa Rosa. Puerto Rican food on the west coast... Good food, relatively small restaurant usually busy says it all.
7) Osake. Santa Rosa. The owner/chef is Gary Chu who has a few restaurants in the area but this is the one where I see him every time I'm there. I used to be a regular at his downtown Chinese restaurant "Gary Chu's" but I think he's had someone else running it the past few years and it just hasn't been the same. Osake (Japanese) however is always good. One of my favorite items is the "Martini Prawns" I believe they serve these at both restaurants.
http://osake.garychus.com/chef.asp
smileys/bigeyes.gif Lee's Noodle House. Now this one will definitely surprise you. It is in the far corner of a tiny strip mall which itself is way off the beaten path. It is (essentially) Viet Namese food and fantastic. It is also very inexpensive. All of which are why it has a regular following of locals that keep it in business despite it being strangely situated.
http://leesnoodlehouse.com/
9) my house. (arguably) The best food in Sonoma County with the occasional visiting chef... smileys/wink.gif kidding