Readers and writers of genre fiction are a charitable bunch. I can't think of a single convention I've researched that didn't have a charity auction listed in the program. Here are a few charitable organizations with a science fiction and fantasy bent.
The Heinlein Society, named for acclaimed science fiction author Robert A Heinlein, is a non-profit corporation that qualifies as an educational charity.
The Education Committee promotes Heinlein's work and ideals put forth in his books. In addition to offering awards and grants, the committee creates guides and provides training to educators teaching Heinlein's work. The Library Program was created to help keep Heinlein's work in public and school libraries, thus making his books available to children and young adults. The society also sponsors academic papers exploring Heinlein's influence on science and space exploration. As an issue that was important to Heinlein, the society also sponsors blood drives.
Visit The Heinlein Society to become a member, donate, participate in a reading group or to visit their forums.
SFWA Literacy Fund is a part of the the esteemed Science Fiction and Fantasy Writers of American organization. The Charity was created to promote literacy in general, but with an emphasis on genre reading. Funds may be given to schools or existing literary charities.
Visit SFWA Literacy Fund for more information or to make a donation.
The Science Fiction Foundation strives to bring together people who study, teach, research or otherwise have an interest in science fiction. This charity, located in Britain, supports a research library in Liverpool and publishes a journal three times a year titles Foundation: The International Review of Science Fiction.
From their website:
The four main objectives of the SFF are: to provide research facilities for anyone wishing to study science fiction; to investigate and promote the usefulness of science fiction in education; to disseminate information about science fiction; and to promote a discriminating understanding of the nature of science fiction.
Visit The Science Fiction Foundation for more information
Association of Science Fiction & Fantasy Artists is non-profit educational organization run on donations and volunteers. The purpose or the association is to generate interest in genre art as well as provide education to artists. They sponsor the Chelsey Awards at WorldCon to recognize achievements in genre art.
Visit Association of Science Fiction & Fantasy Artists for more information (don't miss the wonderful gallery).
The Planetary Society is the world's largest space exploration interest group. Founded in part by Carl Sagan, this non-profit group wants society to have a hand in planetary exploration. Some of their projects include developing technologies, funding astronomers and looking for extraterrestrial life.
Visit The Planetary Society for more information.