Westfield mall near union square is busy busy, fancy fancy, and expensive expensive. Do not drive there, you must take take the BART. The Powell station is about 20 feet from the food court, which alone is almost worth the visit (the food court, not that BART). You will have twice as much fun if you avoid the stress of driving. See more at Bay Area Love Letters.
Pier 39 is a tourist trap, but you might as well walk around it once while you're waiting for a boat ride. The sealions are nifty for a bit and its a good place for a quick, relatively cheap lunch. John's Blog has more.
Coit tower is a semi interesting part of the skyline, its shaped like a fire hose supposedly because the person who wanted it built was a fire bug. Turns out that that rumor is WRONG (see the Wikipedia link), apparently not everything they tell you during the bay cruise is 100% fact. Anyway, you should absolutely not try to drive up there, just park in the neighborhood and walk up the hill if you must. I'm not really such a big fan though, I think you can skip the trip there unless you're really hurting for something to do.
This is the city view taken from a tour boat parked at Alcatraz. Many SF natives will say the tour boats (Blue and Gold or Red and White Fleets are the most popular with tickets ~$20, sometimes you can get them on sale for $15 online) are the most horrible thing you can tell a visitor to go do, but every visitor I've had has enjoyed them, except the few that don't like boats in general. So I say embrace the tour boats, hop on board, and fight it out for the prime spots. Not Only But Also has more on the boats, but don't follow their lead and call it Frisco...
Everyone knows Lombard Street is the zaniest street around! This is a shot from near Coit Tower.
