Grace's Table in Napa sells the best doughnut in the North Bay, rworange noted recently. At a price of $2, the crispy cake doughnut was substantial, and it was even served with its own doughnut-hole sidecar. In rworange's view, the doughnuts at Paisan in Berkeley are better and have superior flavor, but Grace's Table is as good as it gets in the North Bay.
There does seem to be a glut of good doughnuts to be had in the East Bay. In 2011, hyperbowler recommended Andy's Donut Stop in Richmond for its jelly doughnuts, which have the perfect jelly-to-dough ratio and a lovely texture that's somewhere between firm and chewy.
In the same thread, rccola noted that Hopkins Street Bakery in Berkeley sells handmade yeast-risen doughnuts, which are "like homemade donuts from the 50s and 60s." The flavors—including raspberry jam, lemon curd, and Italian pastry cream—paired with fresh dough result in a far superior product than the usual artificial-tasting mixes employed by many Bay Area doughnut shops.
Grace's Table [North Bay]
1400 Second Street, Napa
Paisan Pizzeria [East Bay]
2514 San Pablo Avenue, Berkeley
Andy's Donut Stop [East Bay]
971 23rd Street, Richmond
Hopkins Street Bakery [East Bay]
1584 Hopkins Street, Berkeley