PDF signing

There are free programs available to create digital signatures with certificates on PDF documents:

Libre Office

LibreOffice can sign PDF documents since version 4.5.

Portable Signer

GUI and commandline tool for Linux, OSX, and Windows

jPdfSign

A command-line application written in Java which allows to add an invisible signature to PDF documents

JSignPdf

A Java application which adds digital signatures to PDF documents. It can be used as a standalone application or as an Add-On in OpenOffice.org

DigiSigner

A Java GUI application which lets you open PDF documents and add visible and invisible digital signatures to them. Supports smartcards. Available for Windows, Mac and Linux.

CAcert PDF Signer

Command-line tool only for Linux, OSX, and Windows

OpenSignPDF

Supports Smartcards and Timestamping

Footprint

PDF Writer and Signer

PDFCreator

PDFCreator easily creates PDFs from any Windows program.Use it like a printer in Word, StarCalc or any other Windows application.

Misc