northern california, san francisco, yosemite park, and wine country?

For Yosemite, Oakhurst would the cheapest city with a variety of hotels/motels. These are just basic roadside name type places. It is an hour and a half Yosemite Valley from there.

If you're into semi-roughing it you should look into the tent cabins and Camp Curry. You need to book very early for these so look into it now. Basically you get a private cabin which includes a cheap bed and blankets. Bathroom and showers are in a common building. Food is available in the area as well.

I usually end up going to Yosemite View Lodge. Prices are reasonable for the area and it is a little easier to get reservations than inside the park. (Still check early since you're going at a busy time.) It is just outside the Hwy 140 entrance and only 20 - 30 minutes from the Valley destinations. It's a nice drive. They do have 2 places to eat there if you get stuck. Cedar Lodge is another 8 miles down the road as well.

I will only answer about Napa Valley as others pretty much summed up Yosemite except to say use the free shuttle in Yosemite as much as possible.

In Napa Valley the least expensive places to stay that are nice would be at the South or the North end fo Napa Valley so:

The South end, try Chablis lodge,Fairfield Inn,Gala Napa Valley Hotel, Holiday Inn Express & suites, & Napa Springhill Suites.

In the North end, try, The Lodge at Calistoga, and the Best Western Stevenson Manor.

The ones I listed in the South end are mostly in a town just South of the Napa Valley, but only a few minutes drive from the actual town of Napa