Version 0.6.0 of PHP_CodeSniffer was released today. Besides a few bug fixes, support on Windows was improved greatly thanks to patches from Carsten Wiedmann, and a new command line argument was added to stop directory recursion.
From the end user documentation:
If you do not want sub-folders checked, use the -l command line argument to force PHP_CodeSniffer to run locally in the folders specified.
This allows you to specify a list of directories on the command line and stop PHP_CodeSniffer from checking their sub-directories.
You can download the new release, and view the changelog, on the download page.