Check out the tours offered on grayline: http://www.sanfranciscosightseeing.com/sightseeing.cfm

I assume they use a standard bus rather than an open air vehicle.

1. Muir Woods is worth seeing.
2. If you have never seen Yosemite consider taking the (all)day tour to visit it. One of the most spectacular places on earth in my opinion.
3. Monterey/Carmel is worth seeing. I will observe the guided tours take one on the "17 mile drive" which is very nice but if you rent a car I suggest visiting the Point Lobos State Preserve instead of or at least in addition to the famous 17 mile drive: http://pt-lobos.parks.state.ca.us/

I have stayed at the Harbour Court twice, both times booked through Priceline. The hotel used to a be a YMCA and the rooms are small, very small. The drawers are under the bed because there is no room anywhere else. Pack lightly. There is no place to stash a suitcase.

Having said all that, we enjoyed our stay both times. The hotel's "back door" leads out to the Embarcadero, only a block from the Ferry Market building. The service at the hotel is lovely, very helpful. They have a wine/beer serving in the early evening in their small but warm and welcoming lobby area. The bathrooms were almost larger than the rooms! :) We basically use our hotel as a place to sleep and shower so it was great for us.

If you are looking for a romantic place to propose, on the water at sunset would be beautiful. We took a sunset/fireworks cruise on the Hawaiian Princess and it was incredible. She doesn't sail out of Sausalito anymore but surely some SF regulars can help you with a romantic sunset cruise.

You can be near the wharf without wharf prices. I like the Cow Hollow/ Marina area. The Coventry Motor Inn and Chelsea Motor Inn run 80 - 90 ish with free parking. And are an easy 3 block walk to the shops and dining on Union Street. They are on busy Lombard Street, however you can ask for and typically get a room away from the street.