I'd also have to say that Amnesty International is too mired in politics to be a sound choice.
Moderate environmental groups might be good, similar for the medical charities. However, if you want to keep the charity in theme with the site, find a charity focused on education or literacy. Reading is fundamental, you know.
There have been some great suggestions, and I've checked out the websites of all those I could find. I've made the choice of charity - we're going to go with Medicins San Frontieres. Their website is at http://www.msf.org/ (for those who missed it above).
I'll close this thread now. That's one decision made, a whole load more to go!