Rabbit
I shouldn't be helping you because you've been a bit of a tard in the past, but... all sins forgiven!
I've been to SF many times since 1997. It's one of two cities I know (NYC is the other) where having a car counts against you. So if you're taking a car and plan to stay downtown, parking is horrendous, and expensive. Fisherman's Wharf is a more attractive area to be than downtown anyway, but there can still be parking problems and great expense.
If you're taking a car, I would stay at one of the motor hotels in the Cow Hollow district on Lombard, which is route US-101 through the city and leads out to GG Bridge. Here's a crappy pic of one I stayed at in 1999 (taken with equally crappy camera). I think this is where I stayed the day before I went out to Lazs's place in Oct., 2003.

From here you can walk back one block to Chestnut St., and get the #30 Stockton bus to Ghiradelli Square/Fisherman's Wharf, or stay on it to downtown. Or you can take the #22 Fillmore trolley bus and transfer to a crosstown route to get downtown.
I like Cow Hollow. It has a nice neighbourhood feel, and plenty of facilities. You can leave your car safely in the underground garage at no extra cost. This is useful because downtown SF really isn't very car friendly.