I've heard raves (on this board and elsewhere) about the doughnuts at Boonfly Cafe (at the Carneros Inn on the Napa end of Carneros).
Napa locals eat plenty of traditional doughnuts at Buttercream Bakery. Some say they aren't as good as the old days, but my husband (the household doughnut freak) says they're superior to most doughnuts.
In a recent breakfast at Parkside Cafe in Santa Rosa, my husband and I had a pullapart, which is Parkside's version of a homey doughnut, and is described in this thread: http://www.chowhound.com/topics/40881...
I am not sure what you mean by homemade but the French donuts (particularly the Chocolate & the Glazed) at Tan's Donuts at the Montecito Shopping Center (Montecito & Middle Rincon in Santa Rosa) are uncommonly good. They have an addictive eggy dough, but they are dished out of your typical low end, Vietnamese owned strip mall donut shop... so I am not sure if they qualify for your definition of homemade.
I also like the sugar donuts at Panaderia La Mixteca on Highway 12 near Izzy's and Hot Dog City in Sonoma... but not nearly as good as Tan's