When D and I got married, we decided in lieu of gifts/trinkets to our guests, we would make donations to charities that meant something to us. Having recently lost my aunt to thyroid cancer, one of the organizations we chose was the Light of Life Foundation. You can read more about the organization here: http://www.checkyourneck.com/.
The other organization we knew would create a bit of a stir. We chose Freedom to Marry. If you follow me on Twitter, you will see that I follow a few "gay marriage" or "marriage equality" Twitter users. This is not by accident. D and I are both avid supporters of marriage equality. Now we knew people would react to choosing this charity. Fortunately, all the feedback we heard was positive. There probably were people who didn't agree with our decision, but they chose to keep it to themselves.