San Francisco is basically divided into several districts. I definitely would plan your trip itinerary with that in mind. I also would consider renting a car for a few days. There are a lot of transportation options in some areas and none in others. When choosing accommodations, I would look at a map and pick a hotel that is near the trolleys lines or some kind of public transportation. I had accommodations in Union Square which was great; lots of bars, places to shop, and buses and both trolley lines run through this district.
San Francisco has much to offer and it is nearly impossible to do everything in one week, especially if your itinerary includes excursion tours. The following are San Francisco essential experiences.
Fisherman's Wharf is a complete tourist trap, but it is where to catch the boat to Alcatraz, see pier 39, visit Ghirardelli’s, and do your souvenir shopping; and if you want real Irish coffee, visit Buena Vista. Once you’re at the far end of the Wharf near Ghirardelli’s, you can walk a few blocks to Lombard St, (crookedest street). Warning: the few blocks are extremely steep and uphill. When in Chinatown, enter where the gate is, on Bush and Grant, visit the Golden Gate Fortune Cookie Factory, and eat some dim sum. Coit Tower offers great views and is in the North Beach area which has lots of cafes, Italian restaurants, and if you’re in the area, check out St. Peter and Paul church. In the Mission District, all you Hitchcock fans should check out Mission Dolores' cemetery; filming location of Vertigo. Also check out Balmy Alley and make a stop to try some tapas. While in the chic Haight-Ashbury, district do a little window shopping, definitely try a crepe, and check out some famous hippy sites – (http://www.43places.com/tag/hippie+history/1338862). In the Golden Gate Park, a definite must is the Japanese Tea Garden. Visit the Embarcadero and stop by the Ferry Plaza Farmer's market. If you have an afternoon free, walk across the street to the Ferry Building, grab a bite to eat and take a ferry to Sausalito. If you’re into art, definitely check out SOMA and The Legion of Honor.
The scattered isolated sites and stuff to see on the western side of San Francisco is when a rented car comes in handy. Transportation is these areas seems to be scarce or nonexistent. First, there is Alamo Square where Postcard Row is located. Then there is The Palace of Fine Arts which is great for pictures. Finally, I highly recommend Queen Wilhelmina tulip garden & Dutch windmill (check out my pics)! Also, if you just walk across the road, the beach and the Pacific Ocean awaits. Since you’re already in the area, eat at the Cliff House bistro. This bistro has great views of the ocean. I was lucky enough to have the sun setting while I was eating. They also have a restaurant there, but the bistro is less expensive.