We would like to announce the availability of free PDF signature applications:
PortableSigner from http://portablesigner.sourceforge.net is a nice application with a GUI.
CAcert PDF Signer is an older, commandline only application.
Both applications are running on Java, and use the iText library, and should work on Linux, MacOSX and Windows.
http://wiki.cacert.org/wiki/PdfSigning