What we need is an affiliate website with charity payout. In short, customers shop through our site and a percentage of the affiliate fee goes to the charity of their choice (if the charity is registered with us). We give a portion of our payment (as an affiliate) to the selected charity. A good example is www.iGive.com.
Obviously, a powerful back-end with reports is necessary to keep track of all sales, which charities get what % of money, etc.
We would like to be able to add any affiliate on our site, not just those at LinkShare, CommisionJunction, etc. and would prefer the site be done in PHP/mySQL.
Thanks for your interest!