15

I had a good experience at this hotel in San Francisco a few years ago. Small and quaint, and near Union Square:
http://www.goldengatehotel.com/

16

I went to California for my honeymoon in August/September, great choice! We didn't stay in Napa, we stayed in Mendocino which is right on the coast and seemed a little cheaper than Napa but still had good wineries around (though I'm no expert!). On your budget you may struggle to find a nice place in wine country though, it is ridiculously expensive, maybe try and eke out a tiny bit more?

Second the poster who suggested the Golden Gate Hotel, for San Francisco it is cheap (relatively speaking, we paid about $180 a night I think) and a really nice little place. It also has a cat and visiting dogs.

We also went to Yosemite, we (foolishly) elected to stay outside the park, admittedly only a fraction outside of the park but given the traffic in Yosemite it takes a while to get anywhere. It was a good deal cheaper than the likes of the Ahwahnee which is a real luxury option, we stayed at the Tenaya Lodge which was kind of cheesy but a good deal. It took about an hour to drive from there to Yosemite Valley, but it was really close to Mariposa Grove for example.

17

If you want to chance it a night or two (to save money for a few special places) I would HIGHLY recommend the site http://biddingfortravel.yuku.com/ to get priceline rooms in the 3-5 star category. I've rarely ever been disappointed with priceline, but they are all chains, which in this case can be good because there is a certain level of expectation. Sheraton, Hyatt and the like. IF you do the bidding unseen, it will be a specific area, but you also can't back out, they are not cancelable.
I'm not using it because many of these on the coast and SF only promise double occupancy, and there are 4 of us.
I also found this place, don't think we can afford (timewise) this trip, but looks very cool for a honeymoon night.
If you stay there, you can get into a magic show. What do you think, Clodbod? http://magiccastlehotel.com/