The UU church in downtown San Jose is fairly large and active. I used to go there sometimes a few years ago. They had (and I presume they still do) a very active pagan group. I just noticed on their website that they recently called a new minister, who will start in summer. I know nothing about her, but based on the congregation, I would guess that they called someone good.
http://www.sanjoseuu.org/There are a couple other UU groups in the area, a UU fellowship in Sunnyvale and another (not sure if it's a fellowship or a church) in Los Gatos. You can find them both by doing a search for a congregation on the UU Association website
http://www.uua.org/index.html . The Sunnyvale group is small and meets in a room in another kind of church. I don't know anything about the Los Gatos group. Further away, there is a large UU church in Palo Alto, where a pagan group (Bay Area Pagan Assemblies) has a well-attended montly circle. I think BAPA has a website but I don't know the URL.
There are a couple other churches you might consider, that are open to many paths of spirituality.
The Center for Spiritual Enlightenment (
http://www.csecenter.org/) is a large congregation with a very lovely church and grounds in the Rose Garden area of San Jose. Imagine a sanctuary with a huge mature redwood tree growing right in the sanctuary and up through the roof! They are an independent branch of followers of Paramahansa Yogananda ("Autobiography of a Yogi"), who brought eastern philosophy and religion to the U.S. from India in the early 1900s, and they are a very eclectic and welcoming group with a lot of programs and classes.
Unity: Formally Christian but in Unity churches in California you will find ecelectics of all sorts and won't hear anything about sin and damnation, not even much about Jesus. There's a small one that used to have services in Le Petite Triannon Theatre in downtown San Jose, but they now meet at Fremont High School in Sunnyvale (
http://www.unitysilicon.org/ ). There is a very large and very active Unity church in Palo Alto. I don't have their URL handy but I'm sure you can find them from the Unity website
http://www.unity.org/ .
Religious Science: There's one large and active Religious Science church on Clark St. in the Willow Glen section of San Jose and several smaller ones. You can find them from the United Church of Religious Science (
http://www.religiousscience.org/ ) and Religious Science International (
http://www.rsintl.org/ ) websites.
There are a bunch of little pagan groups in the area that meet in people's homes and tend to come and go. You pretty much have to find them through a friend of a friend or on internet pagan networking sites. You might make connections at a BAPA event (mentioned above).
Oh, there are a couple monthly drumming circles around, one at the Divine Science church on Hicks Ave. in San Jose and one at one of the Palo Alto churches, but I forget which one.
Obviously I've been around the block a bit with San Jose area churches, and haven't really strongly connected with any. I think I want to try the Center for Spiritual Enlightenment some more.
A couple other large annual pagan gatherings worth a mention: The Ancient Ways festival is coming up in June at Harbin Hot Springs (I'll be there) and the Pantheacon convention in San Jose (President's Day weekend every year).