There are several organizations that I work with and know that they could utilize the money for a greater purpose. For example, Samaritan's Purse (they help in a number of different charities from sending shoe boxes filled with gifts to children to finding new hearts for people in third world countries who would otherwise die). Another group is Compassion International. My husband and I support 2 children through them (one in Guatemala, the other in El Salvador) and the opportunity to give children a better life is hard to pass up.
Outside of those, I would donate a large portion to my parents. Not as a "pay back" for what they have done (I would never be able to reach a high enough amount) but to fund their calling of creating a "get-away" for missionaries and pastor's on furlough as well as expanding an educational program to teach people the importance of agriculture and ways to create their own food sources. They in themselves are a worthy investment.
Ultimately it is all to the kingdom of God and I would try to honor him with the gift of the million dollars, wherever it came from.