When you want to annotate PDFs using Ubuntu linux you've got the following possibilities:

• PDFXChange under WINE product page PDF XChange Viewer
• xournal user manual wikipedia entry
• evince - not yet having the needed capabilities (but they are planned for the future)

install PDFXChange

cd ~/Downloads; wget http://www.docu-track.com/PDFX_Vwr_Port.zip; unzip PDFX_Vwr_Port.zip

use PDFXChange:

wine ~/Downloads/PDFV_Portable/PDFXCview.exe