I've been to San Francisco a couple of times now; it's an interesting town for sure. Last time the wife & I were there (wife was attending a visual literacy conference) was the same weekend as the gay pride parade... it was ummm interesting to say the least.
Napa is cool & very scenic, we did the wine train tour which is a little pricey but well worth it IMHO. If you rent a car & drive yourself, stay away from the big name winery's, for the most part they are just too "corporate feeling. You'll have a lot more fun checking out smaller places like Ravenswood & Frog's Leap.
China town is well worth a look, but the main sreet is pretty touristy but cool for some cheap souveniers. If you want a real taste of the neigborhood go a block or two off the "beaten path" and check out a Chinese pharmacy. Little Italy is right next to Chinatown & is worth a look too, esp if you're into coffee.
Fisherman's Wharf is cool too, but the "main" draw Pier 39 is VERY corporatized tourist trap but the San Francisco Bay Aquarium IS worth going to there & you can get a good view of the sea lions who've claimed part of the boat docks. If you want some REAL chowder or crab, check out some of the smaller cafe's & walk-up places closer to the Red & White or Blue & Gold tour ship docks. The ferry terminal is also a nice place to go, it's a little corporate, but if you can go on a Farmer's Market day there'll be some great fresh fruit & food vendors. Last time we went, they had the free range chicken and organic beef vendors directly across from the vegan products booths... there were plenty of dirty looks being passed back & forth along that row.
Haight / Ashbury IMO can be interesting if you're into the punk - alternative scene & there are some good low priced food choices for lunch there (Grill Askew had some great tenderloin ka-bobs & grilled vegetables), but there are a lot of derelicts / homeless / street people there too so be careful & if you go to the nearby park for the Asian garden (very pretty) you DON'T want to be there after dark at all!
Muir Woods is just over the Golden Gate Bridge ($$ toll!) is very scenic & is the starting point for some very cool hiking trails, some which'll take you down to the coastline. Tiburon and Sausalito across the Bay are neat towns, good food & neat scenery but pricey if you wanna shop. The Monteray Bay Aquarium is VERY cool, makes for a nice day-trip... along that route you can check out Carmel & the 17 mile drive as well.
Hope this helps,
Doug C.
Hope this helps a bit