The Javasoftware Discourse Network Analyzer (DNA) is a qualitative content analysis tool with network export facilities. You import text files and annotate statements that persons or organizations make, and the program will return network matrices of actors connected by shared concepts.
PDF Annot is a piece of software that enables you to add audio and text annotation to a PDF. It uses JPedal SimpleViewer and iText library. Annotations are supported by Adobe'sofficial PDF Reader. Report any bug here: krakosia[at]gmail.com