Okular in kde4 does a good job, although the annotations don't show up in other pdf readers unless you print it to a pdf
PDFedit, is for advanced users, and is said to be "the most reliable PDF editor for the GNU/Linux desktop
Free editor for PDF documents. Complete editing of PDF documents is possible with PDFedit. You can change raw pdf objects (for advanced users) or use many gui functions. Functionality can be easily extended using a scripting language (ECMAScript).
A.nnotate.com - Upload - Annotate - Share. Online document review and collaboration - PDF, Word and HTML
Jarnal is an open-source application for notetaking, sketching, keeping a journal, making a presentation, annotating a document - including pdf - or collaborating using a stylus, mouse or keyboard. It is similar to Microsoft Windows Journal and to the earlier Mimeo whiteboarding and Palm notepad applications. There is also a commercial knockoff of Jarnal called PDF Annotator - for $50 you can enjoy a subset of the capabilities that Jarnal provides for free.