The Transbay Terminal is a huge hole in the ground around Mission and First just south of Market in the FiDi. Word on the street is that it will be completed around 2017. The Office of Community Investment and Infrastructure is the city department working on this development.
Wikipedia has lots of info about it.
Here's a good list of all the developments that will be on this site.
There's a temporary terminal during construction. You can get info about where it is, different bus lines, schedules, etc. at http://temporaryterminal.org/.