Most Sonoma visitors are likely to spend a day exploring Napa, which I do recommend. Certainly it is also possible to stay over in Napa. If you expect to tour both Napa and Sonoma, Yountville in Napa County is a nice little town for bedding down. (Note that another option is to visit Napa wineries in day one on the way up from San Francisco and then continue straight on to Sonoma).
In Yountville and St. Helena, some solid hotels include the modern, design boutique Bardessono (www.bardessono.com), and the classic Wine Country Inn (www.winecountryinn.com). In the town of Napa, the Westin Verasa (www.westinnapa.com) is a very good smart luxury option, or try the cozy Carneros Inn (www.thecarnerosinn.com). Id also recommend the ultra luxe Auberge du Soleil in nearby Rutherford.In peak season (August through October, harvest time hits by mid-October), Route 29 can get very busy in Napa. This is one reason I prefer Sonoma, in addition to the latters more rustic charm.
For dining, I enjoyed a few wonderful restaurants. The three-Michelin-starred French Laundry by Thomas Keller in Yountville is of course quite famous. Interestingly the rooms are simple; theres nothing fancy or particularly attractive about the decor. Perhaps they purposefully designed it to feel like a modest living room. Nevertheless, it disappointed in that regard. However the 14 courses yes, 14 small courses were unique and amazing. I did not much like two of the dishes (the small lobster plate, surprisingly, was not prepared well) but the other courses were mouth-watering standouts. The service is more than adequate with multiple servers ensuring everyone receives his/her dish exactly at the same time.
As one of America's finest dining experiences, French Laundry offers a base price tasting menu for $275 but if you treat this as an entire evening of entertainment (and our meal lasted from 6:30pm to 10:30pm) then it does make the value for money ratio more palatable. Unfortunately, the wine is additional. If you do the wine pairing, that will add on 50 percent to the total. All the same, French Laundry is a unique culinary experience and I do recommend it.
For something lower key and easier to snag a table (a reservation at French Laundry must be made up to nine months in advance since there are only about 15 tables) try Bouchon, Thomas Kellers other restaurant in Yountville.
Another superb dinner option is Estate (www.estate-sonoma.com) in Sonoma town. It's located in an old Victorian mansion, and is contemporary and nicely designed. The Continental food is terrific and reasonably priced. I liked the energy there as well.