Okay, so it looks like I have time to come back to this sooner than I thought...
So, in SF itself, I don't know what to tell you to do besides the tourist stuff, but a few tips about that at least...
If you're planning to go to Alcatraz (which you are, whether you like it or not, cause it's awesome), you need tickets in advance, especially during the summer. The island itself is a national park, and there's no entrance fee, but the only way to get there is by boat, which is contracted out to a private company (there's only the one company, so there's no point trying to shop around or whatever). You can buy tickets here:
http://www.alcatrazcruises.com/
If you want to ride the cable cars, you actually don't have to wait in line for ever at one end... just get on at the next corner. I always think it's kind of funny to see tourists wait in line for hours when they could just walk one block and get right on.
If you want good Chinese food, there's a restaurant in China Town called Gold Mountain that has the best dim sum I've ever had, and is ridiculously cheap as well. It's on Broadway, near Stockton, which is at one end of China town. Incidentally, it's the opposite end from the Westfield shopping center, which is where the Powell Street BART station is, but assuming you'll be taking BART into the city, if you walk through Union Square and up Stockton (which is the main China Town tourist street), it's a totally doable walk, and you'll get to see China Town and Union Square.
Fisherman's Warf is like the main tourist spot. I think it's kind of fun, but you probably won't want to spend much time there, either. When you go to Alcatraz, you'll leave from that area, so I'd recommend just checking it out when you go to Alcatraz (I'm just assuming you're going - you actually have no say in that

). Assuming you're taking BART, you can walk to Fisherman's Warf from the Embarcadero station (that's what I always do), or there's a MUNI bus/train thingy that runs along the Embarcadero, which I've never actually tried, but I assume it would work. Also, the Ferry Building is right by the Embarcadero BART station, and it's kind of cool. It's mainly just really expensive/fancy food, so if you're into that stuff then it's great (my dad goes into SF sometimes just to buy specific food items from there), but otherwise it's just kind of a cool building if you happen to be walking past anyway. Also, Ghirardelli Square and the Cannery are down from Fisherman's Warf a couple blocks (away from the Embarcadero BART station and the Ferry Building), and those are cool. And the Ghirardelli store gives free samples when you go in (to the store part, not the restaurant part).
Go shopping, cause the dollar is really weak (thank you Bush), so your money is worth relatively more. Westfield shopping center (and the area around it) is great.
Golden Gate Park is nice. And the Japanese Tea Garden there has really good almond cookies (or at least they did as of last time I was there, which I guess was a few years ago).
In Berkeley, Telegraph Avenue (the part near UC Berkeley) is cool.
Great China (in Berkeley) has really good Chinese food. They also tend to be really crowded, but they take reservations if you have at least six people - otherwise you pretty much have to get there around 5. I don't remember exactly where it is though.
And I could probably keep going with this indefinitely, but I have to go to class. But if you have any specific things you want to know about (besides bars, which I can't help with), then let me know...
Ooh, and come to our Bay Area RYL meet we're planning

Cause so far we only have two people, so we've gotta steal some people from elsewhere...