http://www.circlesanctuary.org/liberty/pagancharitywork.html

Some of those are probably duplicated here:
http://www.witchvox.com/lx/lx_charity.html

More here: http://pagantheologies.pbwiki.com/Pagan-friendly+charities

Pagan Scholarships:
http://www.angelfire.com/ia/Geoff/pagan.html (about 1/3 of the page down, some may have been discontinued)

http://www.flybynightbookstore.com/scholarships.html

http://www.witchvox.com/vn/vn_detail/dt_gno.html?id=13434

http://nyc-ppp.org/html/mjms.html

My personal favorite pagan charity: Act of Kindness

There are others, this is just a few off google…but it seems that a lot of folk do not know about them.