Digital signature or scanned scribble?
Digital signature with certificate
Ok, I think you need to look at the Adobe PDF Library (apdfl). It provides a rich API for PDF processing, and I think (Not 100% sure) it sports signing. All licensing of apdfl, which is priced by negotiation, are handled by DataLogics.
After a quick look in the APDFL technical features I see these lnes that say I cannot use it for Digital signature :
The Adobe PDF Library does not provide access to extended Acrobat functionality such as digital signatures, annotations, or plug-ins
That's a pity. DataLogics also offer a library called DLI, built on APDFL, which certainly does do signatures, but it looks as if DLI might only be used to create new PDF files, not to modify existing ones. But I feel it could be worth asking this question of DataLogics.
But I have found another Adobe product I hadn't noticed before, aimed specifically at large enterprises, but I don't know the supported platforms. http://www.adobe.com/support/training/instructor_led_curriculum/lc_es2.5_introduction_to_d igital_signatures.html
just to let you know that I had a contact with DataLogics who developped a new toolkit that seems to manage digital signature .
Adobe PDF Java Toolkit http://www.datalogics.com/products/pdfjt/
I will let you know the results of my tests in the next weeks.