I've donated books in the past to the troops through Operation Paperback, but there are a number of great organizations that will help you to send books overseas.
GalleyCat did a nice round-up earlier this week:
As the world comes to terms with the death of Osama bin Laden, we should all take a few minutes to remember American soldiers serving overseas. We’ve collected seven different ways you can share books with our troops.
1. E-Books for Troops will help you share your used Kindle with our troops overseas.
2. Operation Warrior Library connects writers with military personnel.
3. Books for Soldiers mails books to troops.
4. Operation Paperback sends paperbacks overseas.
5. Books-a-Million will let you select and purchase Books for Troops in a special program.
6. Operation eBook Drop focuses on eBooks.
7. Follow this Google search to find many more options for sharing books with soldiers.