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File by file encryption instead of filesystem encryption

Are there any cygwin/Windows programs that will encrypt a file, but
leave it usable, similar to what TrueCrypt does for filesystems?

TrueCrypt takes a large file (call it "encryptfs") and mounts it on a
drive (call it "M:"). After you enter your passphrase, Windows sees M:
as a normal drive.

However, encryptfs is still encrypted, and you can copy it to make
encrypted backups.

This is great in theory, but has some problems in practise:

 % Even w/ rsync, even using --partial, copying over a large file is
 slow and prone to errors.

 % You have to unmount "encryptfs" to back it up; otherwise, Windows
 says the file is busy.

So, I was looking for a file-by-file solution, where "encrypt1" would
be an encrypted file, and "myfile" would be a psuedo-file based on
encrypt1 that Windows would see as a regular file.

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