The Naval Research Enterprise Intern Program (NREIP): Application opens in mid October.
NSF Research Experience for Undergraduates (REU): Most applications due by late Jan/early Feb.
List of Engineering programs: http://www.nsf.gov/crssprgm/reu/list_result.cfm?unitid=10006
List of Computer Information Science and Engineering programs: http://www.nsf.gov/crssprgm/reu/list_result.cfm?unitid=5049
Berkeley Lab Science Undergraduate Laboratory Internship (SULI): Applications available Oct. 1 and due by Jan 15.