SF is not as big as other cities. Although generally speaking the longer the better, but I would say you can see the city in 2 days easily.

Favorites:

Fishermans Wharf

Golden Gate (Good views from Marina, Presidio Fort, Baker Beach and Marin County (drive over the bridge, exit towards Sausalito, turn left underneath 101 and then up the hill)

Chinatown

Beaches and Marina

Financial District

Mission District

Don't miss a ride on the cable cars and maybe a trip to Alcatraz.

TT

Hi,

If you are planning for any trip then the first thing that needs to be done is that you should decide the trip duration so that you can plan accordingly in terms of cost and other factors. Once you decide how long trip you can go then it will become easier to decide which package you will opt that various tour operators offer. You can opt 1 day trip to even 10 days trip to San Francisco but I suggest you to go for a trip of around 6-8 days as it will give you the time to visit almost every interesting place. Last year I also had a trip to San Francisco of 6 days. I used the services from a tour operator called Tours4fun. They provided me the excellent tour services which I can only imagine. You can contact them for more information on tour packages available these days or you can go to tours4fun.com to know yourself. Their tour consultant will definitely give solution to each of your query in a very cooperative way. We had a good time while touring last year, the accommodation and ground transportation were good and also the knowledge of tour guide was more than enough. Tour escort were very cooperative and professional. Whole staff was working very hard to make us at ease during tour. We visited a list of very excited places like Hearst Castle, Yosemite National Park, El Capitan, San Diego, West Coast of the United States-San Diego and many other places.

All in all we had a tour which I can’t forget for whole life. I suggest you that you must use once their services then find yourself whether they provide high quality service or not.

If you plan a longer trip you can make side trips to places like the Napa Valley and Carmel.  The drive down through Big Sur all the way to LA is spectacular.  You could book a flight into San Francisco and out of LA, and at the end of the trip make the drive to LA.

 If you like to linger in places, and don't rush from site to site, you'll need more than two days for San Francisco. 

Wow very imformative information, I still cannot decide where to go on my vacation.

Ok, this post is dead, but in case someone's curious and still reading it, I'll note a few things:

 

San Francisco is a very small city by metropolitan standards, but it's very tightly packed. Try going on a ride in the cable cars or on the open bus tours. Alcatraz is still a great tour (do it at night), and the city recently defeated a referendum to turn the island into a "Global Peace Center". Yeah, right. We've the united nations building in NYC for that. 

you can totally miss them: slow, loud and pretty expensive if you ask me. in fact, you're probably faster if you're good on your legs (at least on distances less than 5 stations)
sf cable cars are always to late and mostly overrated - a bit like the apple iphone or the allied invasion in the normandy :)

SF is one of the most beautiful places to visit in the US. To get a preview of how the entire area looks like, check this: http://www.mapjack.com/SanFrancisco

Ah but its part of the fun!

They are part of the "image" of the city, not going on one would be like going to Paris and not seeing the Eiffel tower.

HI

Once in the city do you recomend doing the sightseeing on our own or take some guided bus tours available there? parking is a problem I guess..

You mean the prison? A night tour would be quite the thrill, if so. 

I always try to find a guided bus on the first day or so. They give you a good idea as to how to get around and whas worth looking at.

www.irelandwesttours.com

agree, spending a weekend in san francisco would be more than enough time. things i've done in the past that i would recommend:

picnic at chrissy field, bike tour in and around the city, japanese crepes near the presidio, palace of fine arts for a romantic photo opp, indian food in the tenderloin, shopping in union square and pier 39 farmers' market.

Here are some places that you could go in San Francisco.  You may go in Land's End Park where in it has a number of dimensions and historical perspectives than any other park that i know of. Also the Golden Gate National Recreation Area is simply an amazingly well done area.
Second place that I know is in the Seabright beach where you will see bonfires burning in the pits that they have there and  like beacons of light if you are looking at it from the parking lot. I have had many a bonfire here with UCSC staff, even barbecuing selected foods on a grill.
And the last good place to start is the Marin Headlands which I can say is the best view of the greatest looking bridge in the world. I recently got a chance to head up there and the view just got better and better. The amount of history was simply amazing.

There is a great hispanic art area in San Francisco, I believe it is off of Mission St. It sounds a little sketchy, but if you find it, you'll discover that it was worth the search. It has in an alleyway and close by the art district.