AC Transit
reports its weekday ridership for 2Q 2009 is 236,000, so I'll update the list:
Agency - Average Weekday Ridership
San Francisco Muni - 805,600
Bay Area Rapid Transit - 354,800
Alameda Contra Costa Transit - 236,000
Santa Clara VTA - 143,600
SamTrans - 48,200
Caltrain - 40,300
Golden Gate Transit - 29,600
Eastern Contra Costa TA- 8,700
Livermore/Amador Valley TA - 6,200
Capitol Corridor (shared with Sacramento) - 5,000
Not bad!