So, in more detail: if you're at Fisherman's Wharf, just catch the MUNI bus number 28; from anywhere East, just catch a westbound bus or train for $1.25 and get a transfer, change to the 28 at (state? county?) highway 1 and head South (that is, catch the bus on the far [West] side of the road).
The 28 ends at the Daly City station, at or near the corner of Willits St. and Knowles Ave. From there take the SamTrans 390 for, as I mentioned above, another $1.25; I doubt they'll accept the MUNI transfer as payment but what the hell, give it a shot. The worst they can do is say "no" and make you pay the fare.
The 390 takes you to the Palo Alto Caltrans station near the corner of University and El Camino Real. From there catch the Santa Clara Valley (VTA) number 22 bus for $1.50 to downtown San Jose.
Total cost of this trip: $4.00 as of November 22, 2004 when I prepared this page from data on the web. Greyhound fare, from their site: $5.50. Recommended donation to email@example.com, if this works out for you: 50 cents. Total savings: $1.00.