We did Napa/San Fran a few years ago for a longer weekend.
2 nights in Sonoma/Napa and then 2 nights in San Fran. When we go back it will definitely be just Napa area - I think SF can be seen and done in a few days once.
We stayed at the Marriott Resort in Sonoma and it was very nice and we loved it. Loved that it was in the smaller town of Sonoma and not very touristy. When we go back we want to try and stay in the St. Helena or Healdsburg area - just as others have posted.
We used Platypus Wine Tours but have heard that they have recently gone downhill in terms of tours and service. Have had friends just use Uber and that is probably what we would do if we returned.
On the way up to Sonoma we went to Muir Woods - would highly recommend. It does cost money as it is a national park so be prepared for that. We also went to Santa Rosa to Russian River Brewing and really enjoyed that, we wanted to spend more time in that area.
In SF we did Alcatraz and loved it. The Wharf is VERY touristy; we ate there but I would not recommend it. We have some friends who went to SF in the fall and were disappointed in everything basically because of all the homeless people.
Lauren K '07
www.breezecustomtravel.com
@breezecustomtravel