Sometimes I need to annotate a pdf file, either to take notes or to fill it out as a form since I have ugly handwriting; for the latter, I’m referring to the case where the pdf file does not have form fields you can type in with Adobe Reader. This post describes some programs for annotating pdf files. Xournal is useful when you just want to write on top of a file and print out the content; it converts the content of the original pdf file to an image and saves the old and new contents as a pdf file. I use Xournal on my Asus T101MT touchscreen netbook. Okular seems good except that you can’t save the annotated content and original content as one file or even print the annotated content with the original content.
I just tested Foxit Phantom via Wine and I am able to annotate, save the new pdf file, and print the old+new contents. For form-filling, I recommend printing to pdf as I noticed some glitches with how contents are displayed in the saved pdf files.