National Security Administration Computer Science Internship
"In the Computer Science Intern Program (CSIP), you will gain first-hand experience in critical work at NSA, while making a valuable contribution to national security. And you'll be earning a salary too!
As a CSIP intern, you will have the opportunity to apply your Computer Science skills to NSA hardware and software systems.
Applications are accepted September 1st - November 15th each year."
http://www.nsa.gov/careers/opportunities_4_u/students/undergraduate/csip.shtml
National Science Foundation Research Experiences for Undergraduates (REUs)
"NSF funds a large number of research opportunities for undergraduate students through its REU Sites program. An REU Site consists of a group of ten or so undergraduates who work in the research programs of the host institution. Each student is associated with a specific research project, where he/she works closely with the faculty and other researchers. Students are granted stipends and, in many cases, assistance with housing and travel. Undergraduate students supported with NSF funds must be citizens or permanent residents of the United States or its possessions. An REU Site may be at either a US or foreign location."