This page discusses some of the software libre available for annotating digital documents.
Jarnal
Jarnal is Java-based PDF annotation software. It runs on Linux, Mac OS and Windows.
Okular
Okular is the KDE document viewer. While the underlying PDF reader library Poppler does not yet support annotations, Okular stores inking information its own database. Okular is a part of KDE and as such available for Linux, Mac OS and Windows as part of the KDE suite (sometimes packaged with kdegraphics).
Xournal
Xournal is a GTK+-based inking application. It runs on Linux and potentially on other platforms.