Soma knows what's up.
First, where in the city are you staying? And where in Napa are you goin?
In the city, definitely hit up Toronado, and you can save a trip to Russian River, they have most of their beers on tap, including some bad ass sours. In fact, they have the best taps I've seen in the city. It's a must-stop if you're a beer lover. Grab a sausage next door and bring it in, cash only.
Also, Monks Kettle - one of my favorite places in the city, its in the Mission.
Just a great spot.
Toronado is in lower haight, and you can walk (long but a cool walk) from Toronado to Magnolia in the Haight. Lots to check out along the way, and it'll give you a real great feel for San Fran...plus Magnolia usually has a few on cask, and some decent grub. Jerry's house is 2 blocks from here !
If you're with your wife or something, total tourist thing to do, but go to the Top of the Mark for a $7 Anchor Steam, and some ridic views of the city. Then you can check off Anchor Steam.
If you're stayin around Financial or North Beach, grab a beer at Churchkey on Grant & Green, and walk home.
Have a great time !