Where to stay
There are a number of higher-priced inns and B&Bs that would qualify. A few that come to mind first are The Farmhouse Inn, Honor Mansion, and Kenwood Inn & Spa. At the coast the Bodega Bay Lodge is pretty special. Hotel La Rose in Santa Rosa won't cost as much as the small town inns. If you want seclusion try one of the small establishments in the town of Glen Ellen.
Where to dine
Harvest Moon Cafe, Sonoma
John Ash, Santa Rosa
Madrona Manor, near Healdsburg
River's End, Jenner
Where to visit
Sparkling wine is the wine of romance. Find it in a nice setting at Gloria Ferrer, J, and Korbel. Chateau St. Jean, Ferrari-Carano, Gary Farrell, Matanzas Creek, and Michel-Schlumberger (resv reqd) all have beautiful settings.
Don't forget a walk on the beach at the coast or be there to watch the sun set.
Coming to visit for Valentine's Day?
A number of wineries will be doing something special on the weekend before or on the day of. Check around. Make dinner reservations early!
Going to pop the question?
Lots of couples get engaged here. If you want to use a winery or vineyards remember you are on private property and should ask permission! Some inns offer a proposal package. I'm not aware of any Sonoma County wineries offering a proposal package--that seems to be a Napa thing. However, you can put together your own at many wineries by calling ahead, telling them what you're going to do, and they can have a bottle of wine at a private table waiting for you.