Another nice, scenic drive is to go to the Golden Gate through the Presidio. Use the Lombard Gate, then follow Letterman Ave. (stop by the Yoda Fountain at George Lucas's building if you are a SW fan), then follow Lincoln Blvd to the GG or all the way to Baker Beach.

+1 ^ to Stockton Garage. It's the best located and the cheapest downtown. I also like it because the driveways and parking spots are spacious (at least until the 7th floor).