<p>What tools are available to encrypt or password-protect a file stored on the IFS?</p>

<p>*integrated file-system, accessible from Windows</p>

You could setup object security so only certain users can view the file.
There are encryption tools available for purchase. There is also some built-in APIs for encrypting.
Here are some resources to look into:
Scenario: Key Management and File Encryption Using the Cryptographic Services APIs
The Next Step in Security
A Simple Encryption/Decryption Algorithm for Numbers
Cryptographic Services APIs
Most of these articles deal with encrypting data in a table, but the concepts should help you encrypt a file on the IFS.