Subdirectories:
base --- Binaries for base distribution (managed by Duncan Murdoch). This is what you want to install R for the first time.
contrib --- Binaries of contributed packages (managed by Uwe Ligges). There is also information on third party software available for CRAN Windows services and corresponding environment and make variables.
Rtools ---Tools to build R and R packages (managed by Duncan Murdoch). This is what you want to build your own packages on Windows, or to build R itself.

Please do not submit binaries to CRAN. Package developers might want to contact Duncan Murdoch or Uwe Ligges directly in case of questions / suggestions related to Windows binaries.

You may also want to read the R FAQ and R for Windows FAQ.

Note: CRAN does some checks on these binaries for viruses, but cannot give guarantees. Use the normal precautions with downloaded executables.