BART
Bay Area Rapid Transit (BART) has seven stop within San Francisco, bisecting the heart of the city. Any one-way trip within city limits costs $1.75. For destinations in SF you will generally not wait more than 10 minutes, 5 during peak hours.
BART has good options for mobile access to schedules:
http://bart.gov/schedules/mobile
or point your wireless device to http://m.bart.gov
Bikes are allowed on BART, with some restrictions.
Bus