There are a lot of ways to navigate through the city with a bicycle. Heres a few maps to help.
Ride the City - Shows bikeshare stations, bike routes, and bike shops.
OpenStreetMap Cycle Map- Shows off the bike related features in OpenStreetMap as well as some elevation topo lines.
Bike Mapper via 511- Mostly for routing with options favoring speed or least change in elevation.
Map My Ride Allows users to easily share their favorite bike routes and browse routes in particular areas.
Googley maps bike routing and is the standard bearer for reliably giving you a valid route.
Bay Area Bike Share Stations in SF From BABS.
San Francisco Bike and Walking Guide: In PDF form.
SF Bay Guardian Bike map from May 2011 - Looks like it was put together for bike to work day.
San Francisco Bicycle System- A map of bike routes modeled with a subway map style.
Make a better one with the data provided by the SFMTA on their bike routes and share it here. The SF municipal goverment is even so excited about sharing data there are multiple datasets to draw from:
Plus you could use data from the bike routes in OpenStreetMap or other sources.