Made two big improvements to the Windows port, in just a few hours. First, got gpg working, and encrypted special remotes work on Windows. Next, fixed a permissions problem that was breaking removing files from directory special remotes on Windows. (Also cleaned up a lot of compiler warnings on Windows.)
I think I'm almost ready to move the Windows port from alpha to beta status. The only really bad problem that I know of with using it is that due to a lack of locking, it's not safe to run multiple git-annex commands at the same time in Windows.