"Wine Country" in San Francisco usually means Napa or Sonoma counties, but I'll put notes here on other wineries & wine areas in Northern California...
The eponymous town for Napa Valley is in the south.
Foothill Cafe - Patricia Unterman rec's for its fresh, California cuisine; popular with locals
Bistro Don Giovanni - Patricia Unterman rec's
Julia’s Kitchen - Patricia Unterman rec's
Mustards Grill - Patricia Unterman rec's
Pearl - Patricia Unterman rec's inexpensive VLTs, mozzarella sandwich, smoked salmon, etc.
Gargiulo Vineyards - rec'd by a friend
Elyse Winery - someone said it's "the best place you've never heard of"
Yountville & Oakville
These central towns in the Napa Valley host such famous restaurants as the French Laundry and Bouchon. The nearby Silverado Trail runs up the east side of the Napa Valley, and has slightly smaller wineries (including celebrated ones like Stag's Leap Cellars, which won the "Judgement of Paris")
Bistro Jeanty - Yountville rec’d by Patricia Unterman and http://www.napatouristguide.com/agenda-silverado.html
Oakville Grocery - lots of good meats, cheeses, etc.
Bouchon Bakery - Yountville, good pastries and breads by Thomas Keller (of French Laundry fame)
Bottega - nice spot for California-style Italian
Regusci - nice spot, large tasting room with gorgeous view & porch (call ahead to reserve)
Seltzner - small place, has a good port
Robert Sinskey - nice place, good wine, great place to picnic (no reservations for picnic tables) --> POV Red was in SFGate's top 100 wines
Baldacci - cozy location, tasting fee refundable with purchase, also run concerts in the late summer
Del Dotto - someone rec'd reserving a "cave tour"
Northern Napa Valley (Rutherford, St. Helena, Calistoga)
Cindy’s Backstreet Kitchen - St. Helena
Tra Vigna - St Helena → also has the Cantinetta, a take-out deli
Wappo Bar Bistro - Calistoga
Prager - known for port --> really fun place, one of the few places where we met the winemaker and not a bunch of staff
Peju - known for it's "rapping" wine bar
Round Pond Estate - rec'd by a friend
Rutherford Hill - supposed to be nice for picnicing
A good resource is Local Wally's Guide to Napa Valley (Napa Tourist Guide), which is a relatively unbiased
http://www.napadowntown.com/ “Taste Napa Downtown” gives you 13 tastings within walking distance for $20!
http://www.preiserkey.com/ good guide to restaurants & wineries
Various companies such as Napa Valley Bike Tours in Yountville, let you rent bikes to take to the wineries.
Sonoma Saveurs - sonoma, charcuterie/bistro/wine bar, foie gras
Cafe La Haye - Sonoma
Cheese Shop of Healdsburg
Willow Wood Market - Graton, country-style meals
K&L Restaurant - sebastapol
Alexander Valley (Healdsburg, Geyserville, N of Napa/Sonoma)
Ravenette/Ravenous - Healdsburg, cafe inside Raven movie theater, rec'd by Patricia Unterman
Santi - Geyserville, rec'd by Patricia Unterman
Bistro Ralph - Healdsburg, rec'd by Patricia Unterman
Manzanita - healdsburg
Jimtown Store - Healdsburg, along Hwy 128, known for olive spreads/condiments, also has sandwiches
Bouchon Bakery - Yountville, good pastries and breads
Healdsburg Farmer’s Market, Sat 9-noon
Cheese Shop of Healdsburg
V Sattui, Beaulieu --> ??
Viansa, Cline, GLoria Ferrer - sonoma
other sonoma: *Ferrari-Carano, Kunde, La Crema,Nicholson Ranch,Meeker, and Gary Farrel, Seghesio, Frank Family Vineyards, Armida, Hop Kiln (mostly for the location), Sausal, Ravenswood, Sebastiani
The Girl and the Fig - amazing duck, wonderful other French specials!
See SF Wine Page