Unfortunatly, San Fran is one of those cities with so much to see and do that it's hard to squeeze everything in, even in a week.
If you're planning an Alcatraz tour, which is pretty cool, check into a night time tour. You take the boat out as the sun is setting and the view back from the bay to San Fran is awesome. Alcatraz is a lot cooler at night. They have a self-guided headset tour that shows you just about everything. From there they have individual mini tours you can sign up for. You can't do them all though. I suggest the hospital tour as one. The ship ride back to land is really cool at night with all the lights in the city.
Everyone drives across Golden Gate and goes to a lookout spot there. There is a rest area on the right side as you drive across from the city. It was closed for construction last time I was there though. Anyways, get off at that first exit and stop if its open, if not loop back onto the road to go back across the bridge, but take a quick exit off onto a look out area there before you go back across. You can drive all the way back to the very end of the road(1.5 miles maybe?). There is a really cool spot at the end where there used to be an old gun battery emplacement and tunnel during WWII. You can walk through and look out onto the Pacific on the outside ridge of the Bay. Then you can drive back to various overlook spots all the way back to the bridge.
Golden Gate Park is really neat. They have so many things there. Japanese Gardens, different ponds and waterfalls and trails. The flower conservatory has been renovated totally. A lot of movies filmed there.
Road trips I suggest are to Santa Cruz and Monterey. You can drive down to San Jose and then through the mountains to Santa Cruz. There is a boardwalk there that is neat.(The Lost Boys was filmed there) Then you can drive around Half Moon Bay to Monterey. AMAZING little town there. Make sure you drive around the coast to Pebble Beach. One of the most beautiful spots on Earth.
Lastly, not sure if you're into this sort of thing, but there is a place called the Winchester Mystery House in San Jose. It's a really neat attraction there. HUGE old, very odd house that you can tour through. Supposedly haunted, etc. Built by the Winchester Rifle Coumpany money.... the house was literally built 24 hours a day every day for 40+ years. Look the website up online. Definately worth a stop.
Hope this helps. Any other questions, just ask.
One other thing... no trip to Cali is complete without a stop at In and Out Burger! I suggest a Double Double, animal style, with fries and a large NEO shake. There is one down on the Wharf area downtown.