My fiancee and I wanted to add a charity in addition to our regular wedding registry. So we opened an account with the I Do Foundation. They do a great thing by directing guests' funds to the charity of your choice.
But it turns out that they charge guests 10% of every donation and keep it for themselves! This was very disappointing and I cancelled my registry with them. So I realized I could cut out the middle man and put the direct link to the charity of my choice. This way, I knew that 100% of the donation went directly to my chosen charity. Many charities have links on their site where guests can send an e-card or a printed card to you telling you about the donation:
I am sure others will make special arrangements where they can send cards unofficially.
Also, check the Better Business Bureau before you pick your charity. I later found that the I Do Foundation has a poor rating with them while my charity of choice has an excellent rating. The BBB website will allow you to see where all of your funding will go to support each part of the charitable organization.