The most common proposals are directed either to the Census Bureau, the National Center for Health Statistics (NCHS) or the Agency for Healthcare and Research Quality (AHRQ).  Each has different application processes and guidelines.  These links lay out the essential information: 

Other Helpful Resources:

FSRDC Server Software        
Gauss Stata Matlab & toolboxes PBS Pro Intel Composer XE
NX Enterprise R SAS SAS (Dataflux) SUDAAN
GEODa Tomlab Knittro Madd QGIS
StatTransfer Python - Anaconda Fortran Perl Tex/LaTex