S.L.
I'm from San Francisco and I can tell you that hotels there are EXPENSIVE. Because it's such a convention crowd draw, though, you might score a better deal on a weekend night than during the week. The Courtyard by Marriott is not a full-scale-with-restaurant property but at the weekend they have some good deals. They have a newer property at Second and Folsom that has had good weekend rates. There's also one on/near Fisherman's wharf.
My husband and I once got an excellent deal at the Omni, on California Street, for $139. So they are out there. I like to run a search on Expedia and Hotels.com, then check the hotel's own website. Usually they will match it. If you can get a good room at the Hotel Vitale, GRAB IT! It is right on the waterfront, and you can walk to the Farmer's Market at the Ferry building. Really don't miss that. You can also get the ferry to/from Marin there.
And J. B. is right--VRBO has some really cute properties in great neighborhoods. I personally recommend Russian Hill and North Beach, but there's also the Marina, the Fillmore, Noe Valley...the list just goes on. Feel free to message me if you have any questions...
Sorry so long...one last thing: parking rates at hotels run $30-$40 a day, and sometimes you have to pay that based on where the hotel is located. Sometimes there is a garage nearby (i.e. Union Square area) but you have to check their overnight rates. And don't go for a hotel costing less than $100 a night unless it's a super deal with a brand you trust--some of the other ones rent out long-term rooms to people down on their luck...probably not what you're looking for : ) Have a great time and enjoy! S.