Xournal is software written specifically for tablet computers for hand writing notes, or journals, say. I've used it on my Nokia 770. But it has an excellent feature that makes it useful on a non-tablet computer: It allows you to annotate pdf files! This includes highlighting and doodling. Here is a screenshot.
To install it, download the latest version from the project website. Unpack it and run the script called install-binary.
tar -xzvf xournal.tar.gz cd xournal-0.3.1 sudo ./install-binary