We recommend you guys check out the All Nighter Map from 511 for all your late night transit needs, if you want to take public transportation home.
For SF, traveling late at night is easy with the over 10 routes MUNI offers. It's only $2.25 for adult fare. We personally recommend a Clipper Card for late night travel for ease wit h all the agencies you might take. Please note that MUNI routes aren't that reliable at night and aren't that frequent either.
SF To East Bay
So you're done doing whatever your doing in SF late at night after BART closes. There are many options to get home back to the East Bay. The options are listed below. Cities: SF To Oakland: Take AC Transit 800 SF To Richmond: Take AC Transit 800 SF To Fremont: Take AC Transit 800 and Transfer to AC Transit 801