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
Adobe´s documentation on PDF Security: http://blogs.adobe.com/security/2007/04/acrobat_and_reader_security_do.html
A new software, which I haven´t tested yet: http://www.cabaret-solutions.com/de/downloads/linux
OpenOffice feature request with voting: http://qa.openoffice.org/issues/show_bug.cgi?id=47895