"KDE document reader Okular doesn't just read multiple document
formats; it also allows you to add annotations to files as you read
them. Note that to get this functionality, you need version 0.8,
which is in Ubuntu Karmic, or Debian Squeeze (see my howto if you
want to install this on a Lenny box).
"To bring up the reviews toolbar, go to Tools->Review. You'll
see various highlighters, drawing, and note options down the
left-hand side of the document window. Be warned that the inline
text annotation option will hide anything underneath its box.
Right-click an annotation for a context menu that allows you to
delete it or add a pop-up note. You can view all annotations by
clicking on the 'Reviews' tab on the far left of the Okular