The National Science Foundation, like most government bureaucracies, has a tree-like structure. At top is the office of the director (Rita Colwell). Below that are several directorates including the Directorate for Computer and Information Science and Engineering (CISE) headed by Peter Freeman. By law every organization in NSF cannot be just "science" but "science and engineering" except for the Foundation itself.
Below CISE were several divisions, including Computer-Communications Research (C-CR) headed by Kamal Abdali. C-CR ha several programs including the Theory program headed by Ding-Zhu Du.
Peter Freeman, who recently became head of CISE, has decided to reorganize the whole directorate. Exactly what it will become should be announced next week but there are some hints in this presentation. Change is always scary but I'm hopeful theory will survive. I'll give more details when I know them.
To overcome the tree structure of NSF, there are a number of cross-disciplinary programs. One such program, Information and Technology Research (ITR), has produced several large, medium and small grants to a variety of projects, including many applications of theory. This is the last year of ITR solicitations and the calls have been well behind schedule, probably not unrelated to the CISE reorganization. This year's topic will be on "ITR for National Priorities" with more details promised by Thanksgiving. Unconfirmed rumors have the program will be more focused and only making medium sized grants.