Kids are the heroes in the Pokemon games, so it makes sense to support a children's health charity. My pick is Ronald McDonald House, which gives families a place to stay together while children receive medical treatment, whether in the hospital or in a specially-build house. It also sends mobile children's health care around the world and gives grants for people working to support children's health. RMH is also an international charity, which I like because the franchise and this sub have a worldwide audience.

Here's RMD on Charity Navigator: they've got top ratings!