There are many websites nowadays that promise to help you navigate charities. This page lists some, as well as some charity orgs that I want to log for my own edification.
Civil liberties and other political
Pleased to meet you. I'm a card-carrying member of the ACLU. I'm personally kind of fond of the bill of rights. Like, who wouldn't be?
Choice and women's health
Health issues
Nature
Save trees
Various categories of people
Babies and children
Obviously these categories overlap, but hey.
Hungry people
See also the San Francisco organizations list, below.
People of color
People without houses
I really like Habitat for Humanity. I think that Mr. and Mrs. Carter have done absolutely cool stuff, and it's always nice to hear about their vision being carried out.
People with health problems
Seva is a nonprofit that helps to give the gift of sight. (among other things)
San Francisco/Bay Area-specific Charities and Organizations
Meals on Wheels of San Francisco. Shut-ins. Aids patients, older folks, you name it.
Palo Alto
Here is a recommendation for the Palo Alto area: "I love the Ecumenical Hunger Program in East Palo Alto. My experience with them has been very positive. It's a wonderful direct service option as they accept all household items, clothing, children's books & toys, and non-perishable food items. They make sure all donated items go directly to a family in need. You can drop things off, or a truck will come to you. "
Parks and museums