Here's an economical option in San Francisco that also offers parking -
http://www.cowhollowmotorinn.com/

Here's a moderate option in the wine country -
http://www.jacklondonlodge.com/location.html
Just down the hill from Jack London State Park - A co-worker and I discovered it when most lodging would not allow a 1 night stay on the weekends. Very nice place, good location and we spent the morning at the state park before heading out for wineries.
http://www.parks.ca.gov/default.asp?page_id=25130

Flying into SF around 10am, after a fourteen hour overnight trip from Australia, we've found the CityGarden in South San Francisco to be convenient and reasonable. We catch a free shuttle bus from the Airport to the hotel, dispose of our luggage, and then catch a local bus into the city from very close to the hotel (not outside though). Have a bit of a look around, catch the bus back, have tea and collapse in bed!

This way, we can have a couple of days to get rid of our jetlag, before catching the free shuttle bus back to the airport to pick up our hire car. It works well for us, free breakfast and Chinese smorgasbord restaurant adjacent.

http://www.citigardenhotel.com/

I always stay with my son and daughter in the Mission/Castro neighborhood so I can't recommend a hotel, but here's some advice that will really save you money: don't rent a car at the airport--rent one downtown instead. We've rented with Avis on Post Street (near Union Square) the past couple of visits, for really great prices. Reserve the car now. Compare the prices of airport vs. downtown and you'll see what I mean.

Public transportation in SF (Muni buses, trains, cable cars, BART) is easy to use and takes you everywhere you will want to go. The buses are great for people watching. You don't need a car in town, but it's fine to pick it up there and head out to your other destinations.

I would not spend any nights at the airport. Take the BART into SF for about $8.50 and catch either Muni or a cab to your lodging. Rent the car the next day if you want to get out of town that day. If you're renting from the Union Square area, it might make sense to get a hotel in that area and just walk to pick up the car.

Sign up for Groupon SF to see what their offers are for things to do in SF. Recently there've been half price offers for bike rental (ride across the GG Bridge), Napa/Sonoma day-trips, etc. Might save you money on something you want to do--who knows!

I don't like Fisherman's Wharf at all (way too many tourists, too much tackyness), but it's a good place to catch a ferry for a day trip to Sausalito or to Angel Island for a nice hike around the island. Or you can catch one near the Ferry Building at the end of Market, which has some nice food shops and some days a farmer's market where you can buy stuff for a picnic if you go to the island.

You can happily fill all 8 days in SF itself, but all the other places you want to visit are also nice. Maybe a bit too much for just 8 days...but you know how much driving you want to pack in to what is basically a week. Have fun!

TravelZoo and Hotwire have some good hotel rates. You might want to look at what they have to offer.

In SF, I would skip Fisherman's wharf (very touristy) and Union Square (unless you like to shop). Instead, go to Golden Gate Park. So many things to do there...walk around pretty Stow Lake, rent a paddleboat there, walk over to the De Young Museum (make sure you get the view from the tower) and walk across the way to the Academy of Sciences, which recently reopened and is fantastic. You could also combine a museum stop at the Palace of Legion of Honour with a hike along Lands End (specatular scenery, can start walking from the museum). Lombard Street is beautiful (the twisty part), but walk it instead of driving it. If you have time, go to Coit Tower from there for some great views. Alatraz or Angel Island from the ferry would also be a fun choice. Have fun.

I prefer the Sonoma Valley to the Napa valley because it has both wineries and more history (the town of Sonoma and its square, Jack London State Historic Park, Gen. Vallejo's house).

As for less expensive hotels, aside from deals and bidding on Priceline and other similar sites, you could try the motels near the zoo (Wawona or Sloat Blvd. around 45th Ave.) or near the ocean just south of Golden Gate Park (Irving or La Playa near 48th Ave.). Both of these locations are at the end of a MUNI line that would take you downtown.

I also prefer Sonoma Valley to Napa, but I'm not so interested in wine tasting === just like the small towns, and in particular, Healdsburg (although we like Sonoma, too, and in Napa, St. Helena and Calistoga are nice).

As for Michael's other suggestion, I definitely would NOT suggest this. It would take more than an hour each way to go by bus from out near the zoo to downtown. IMHO, not a good location unless you need/want to be out there for some reason.

There is an option to get to Yosemite without renting a car in San Francisco. An Amtrak bus leaves Fisherman's Wharf early morning and goes to the Jack London Amtrak station. Ride the San Joaquin to Merced and rent a car there or ride the bus to the valley. The other place to rent a car is at the Fresno airport and come into Yosemite from the south entrance.
For your trip to Sonoma or Napa you should rent from a downtown SF location to save money.

I would take the L Taraval or the N Judah, both of which are close to the motels.

Why would anyone choose to schlep five different transport legs -- 1) Bus/streetcar or taxi to the Wharf (or to the Ferry Bldg), 2) bus to Oakland, 3) train to Merced, 4) bus or taxi to car rental agency 5) rental car to YNP -- when the alternative is to jump in a car in SF (or at SFO) and get out of the car in Yosemite Valley.

Not only would it be a slog -- it would take much more time . . .

Amtrak is definitely an option for some journeys -- this ain't one of them. (The only exception is someone who cannot drive/rent a car for some reason)

Thank you everyone - still need more help about hotels. We have definitely looked at all the sites, but need more information by your experience.

We don't mind being in a touristy area, because we do want to do the touristy stuff. We are leaning against Union Square now because we don't have interest in shopping.

Can you recommend a hotel that is clean, reasonable, close to the trolleys or the BART, and has free parking and breakfast? And also is safe for two young women? (we are NOT party-ers by any stretch). A specific hotel name and area would really be helpful.

Also - didn't really get a response to the order of our trip...when should we travel to the different locations. We arrive late Wednesday night the 13th of July and leave the following Thursday. If anyone has insight on my initial 3 numerated ideas above, please share.
Thank you so much!!!

What did you think of the Cow Hollow suggestion?

You might check Hotel Chancellor on Powell near Union Square:
http://www.chancellorhotel.com/packages2.htm
DH and I often stay there when we can get the package that includes parking (off-site, but convenient). It's not fancy, but nice enough.

Also, check lodging in/around Yosemite ASAP, as it is a very popular park and lodging can be difficult to find in the summer.

most hotels in the tourist areas (with exceptions above) do NOT have free parking. Parking is VERY expensive here and hotels can get away with charging an arm and a leg.
Same with breakfast - a lot of hotels have rates that include breakfast but the charge is way more than a breakfast would cost...

I don't normally recommend Travelodge's but there is one travelodge in SF that might work for you(only this specific Travelodge --there are others in not as good locations)

http://www.travelodgepresidio.com/

This one is at the very end of Lombard street just outside the Presidio. Walking distance to the Disney Museum and other sites in the Presidio, the Exploratorium/Palace of the Legion of Honor, Marina Green, Crissy Field and Fort Mason.

Easy car access to the Golden Gate Bridge, Fort Point, the Wharf, and lots of other places.

Free parking, and a decent continental breakfast -- more than the average budget motel provides, w/ coffee, tea, juices, cold cereals, pastries, fresh fruit, and a microwave to make things like instant oatmeal.

The rooms are small-ish but have a coffee maker, fridge, and updated bathrooms w/ nice towels, surprisingly high end toiletries, hair dryer, granite counters. Not posh by any means --but a good location and better than one might expect at a travelodge.

Good suggestion janis, while it lacks charm it's in a good, safe location.

babs,
As you said...I would do the car trip part all togehter and ditch the car in SF. You won't really need it or want it! That way you don't have to worry about finding someplace with free parking. You can get a multi-day transit pass for a reasonable price.

It's been years since I've been to SF, but I stayed at the Chancellor and it was very nice. Rooms are small and baths are smaller, but it is extremely convenient and still gets great reviews. Don't base anything on an included breakfast because my most recent research indicates that is not a real selling point.

Try TheMosser.com for great location, clean [small] rooms. They have rooms with hall showers [that are very clean and well maintained] and can be a real bargain.

For unbeatable bargain and great way to learn the city, try free [donation only] CityGuides tours offered by SF Public Library. http://www.sfcityguides.org/

Free tour of City Hall is very good, watch the movie, Milk, first.

Head up to Berkeley via BART for a different view of life in the area.

Walk across Golden Gate Bridge, go to Sausalito and then take the ferry back.

starss - my friend wasn't really digging cow hollow. i'm a little more adventurous on hotels than she is - she has more money to spend! so i'm looking for a safe, clean, great deal. thank you though for your suggestion!

kathy and janisj - will definitely check out your suggestions, thank you! i think we had seen the chancellor before on tripadvisor or something. and what you said about the travellodge sounds promising.

deb - okay so do we do the driving first or last? i'm thinking do san fran city stuff first, get the car on our 3rd full day (maybe midday) and then head driving. but what route to take? napa, then yosemite then the coast? backwards?

thank you so much everyone!!!!

babs,
I think the order is strictly up to you and the activities that are important during your trip.

I'll be visiting CA with DH next month and we will fly into and out of SFO, but will go directly from the airport to Pacific Grove. We originally thought we'd do the Monterey Penisula mid-trip, but the logistics didn't make sense. See my thread "Northern CA trip".

We aren't trying to include Yosemite because fitting all the things we want to do into 6 nights is already a problem!

Too bad you can't go a little higher on your budget...Union Street Inn in Cow Hollow gets great reviews and includes breakfast. I don't know about parking.

Frankly, I think the biggest lodging question for you is Yosemite, not SF. At this point, it's doubtful you will be able to get anything except perhaps a tent cabin in the park itself - the hotel rooms sell out very quickly. I personally really dislike the tent cabins, mainly because they are so close together you really have no privacy, but if you're only there one night, maybe that's okay. But I would check on the availability of lodging right away. You may end up having to find a room outside of the park, and that can be a drag - it can take anywhere from 30 minutes to more than an hour to drive into the valley just from the park entrances, depending on the time of day and how bad the traffic back-up is.

When I went to Yosemite, we were not able to stay in the park. But the place we stayed was pretty nice and convenient. I'll try to look it up. Not that it's still there, but the area would work.