How to highlight and annotate PDF and DjVu documents?

Okular can be used to view, highlight and annotate (with sticky notes) both pdf and djvu files. After opening the document in Okular, press F6 (or Fn key + F6). The controls to highlight, annotate will appear(along with some more tools).

A small hitch: By default these annotations are stored outside the document. So if you mail the document to somebody, he/she will not be able to see the annotations/highlights. But there are ways around this problem (as described in the official help page of Okular)

Try Xournal:

Xournal is a GTK+ application for notetaking, sketching and keeping a journal using a stylus. It can also be used to add annotations to PDF files.

Try PDF-Xchange Editor and zathura. It allows you to open multiple files in tabs and functions both as a good viewer. It stores annotations/comments within the file.

To install in Ubuntu follow these instructions