There are 2 free programs available to create digital signatures with certificates on PDF documents:
"Portable Signer" (GUI + commandline for Linux, OSX, Windows): http://portablesigner.sourceforge.net
"CAcert PDF Signer" (commandline only for Linux, OSX, Windows): http://www2.futureware.at/svn/sourcerer/CAcert/PdfSigner/ Nautilus Script for PdfSigner: http://www.cacert.at/svn/sourcerer/CAcert/PdfSigner/pdfsigner-nautilus.sh
A new software, which I haven´t tested yet: http://www.cabaret-solutions.com/de/downloads/linux