Serious Eats - seriouseats.com

I was just in San Francisco in January. My favorite places were:

Slanted Door - make a reservation far in advance, but the food is amaaazing!

Magnolia - brewpub in the Haight, right near Haight Ashbury - great homebrew, awesome burgers, cool atmosphere

Victorian Punch House - also right near Haight Ashbury, no food, but worth the stop (especially during happy hour!)

Fisherman's Wharf - right next to Boudin are a bunch of stalls that sell Clam Chowder in a bread bowl.

Try any of the OSHA Noodles locations - they vary from hole in the wall (near Union Square) to almost fancy. Actually, come to think of it, most of the noodle places we went to were cheap and fantastic.

Also, try to stop by the Gold Dust Lounge near Union Square during happy hour - $2.50 margaritas and some serious dive bar atmosphere. It's awesome.