Xournal is an application for notetaking, sketching, keeping a
journal using a stylus.  It is free software (GNU GPL) and runs on
GTK+/Gnome platforms.  It is similar to Jarnal, Gournal, and NoteLab.

Xournal allows to add annotations to PDF documents, including notes,
multicolor highlighting and simple drawing, and can save those in
another filename (distinguished by the suffix), to automatically
load them back when opening the PDF document again.  It also
remembers the previous page position.