So I got in touch with a couple friends & have an even larger list for you! Restaurants: Frances, House of Nanking, Bar Crudo, Beretta, Wayfare Tavern, Mama's, Saigon Sandwich, & Sushi Zone. Hopefully this helps! You'll love SF!
Try Chow! I always go to the one on Church St. It's really good comfort food, great cocktails and they're open all day. It's in Castro, so there's also a lot of great bars in the area and you'll be away from the wharf/touristy areas.
The Parlor is a new and stylish addition that seems to be all the rage in San Francisco. Fusing an ultra-retro atmosphere with the modern nightlife style, the club features plenty of private booths for outings with company, and a lounge area for singles. All in all, it's a posh place to check out.
Avoiding tourist traps is a fairly easy task in San Francisco. A street car is a street car, and Fisherman's Wharf is nice, sure, but there's a lot more to the city than clam chowder and old fashioned mass transit! On my last visit, besides the tourist traps, I had fun racing my friends up the "world's most steep hill," a great meal at Lers Ros Thai (that's just one restaurant, hit as many as you can!), and a surprisingly impressive visit to Chinatown.
Pacific Beach boasts a very decent array of spa's, many of whom are directly on the water. The Pacific Terrace Hotel is a hidden gem and a favorite amongst San Diego locals, but the Paradise Point Resort is a more popular tourist trap. They're often right next to each other, though, so a few minutes of window shopping might help you spot one at the right price point.