A good kayak link
We often paddle kayaks with Brian and Janet. Brian has been writing about his various kayak trips in a web site, and has recently updated them. His new web site lists many of the places which you can launch from in the SF Bay.
Here is one location that he writes about, and one I have been to a few times also - the South Bay Wreck. This involves paddling out to visit the wreck of the USS Thompson, a destroyer that served between World Wars I and II, but now sits half destroyed in the middle of the bay.
He also has a page that talks about various trips he/they/we have taken at http://gotoes.org/kayaktours/index.pl. With his web site updates, I suspect there is a chance that this site may go away or get a changed address.