If you are a Java or .NET developer, all the following articles are useful for you.

How to sign a PDF using iText and iTextSharp

if you just want a free Digitally sign PDF tool, try the following ones:

PortableSigner-Tool to sign Portable Document Files (PDF)

E-signing PDF documents with iTextSharp
Sign PDF online, but do not know how [...]

Yesterday, I got a email, he said he want a tool to sign PDF in ubuntu. At first, I decided to develope one, then I thought I have downloaded a this kind tool before, so I think just need tell him this one is ok. And if needed, I can compile it with GCJ(of [...]