From Ubuntu 12.10, Okular supports annotating and highlighting pdf files.
After annotating, you should save your pdf file using "Save as ...", so other pdf viewers would be able to read annotations.
From the Ubuntu Forums Code of Conduct.
If a post is older than a year or so and hasn't had a new reply in that time, instead of replying to it, create a new thread. In the software world, a lot can change in a very short time, and doing things this way makes it more likely that you will find the best information. You may link to the original discussion in the new thread if you think it may be helpful.