PDF Annotation Software

Currently, it is not possible to electronically "write" on documents in PDF without the additional software. A number of inexpensive software solutions are available, with features varying from the ability to simply add handwritten or typed text to more complex tasks such as changing the text in the document, adding comments in new text boxes, or inserting common shapes or symbols.

Commonly used programs and related support

Acrobat Pro (cross platform) from Adobe
Tutorials and online documents at the Adobe Learning Center
iAnnotate (cross platform)
Forums, online documents, and e-mail support.
"Branchfire was founded on the belief that productivity and collaboration technology should reflect the way that we think rather than the way that computers and systems force us to work."
PDFpen (for the Mac) from Smile Software
Video tutorial, FAQ, help files, screen shots of basic tasks
PDF Annotator (for Windows) from Grahl Software Design
FAQ, screenshots, online manual
Skim (for the Mac)
Manual, wiki, and screen shots are available at the main website

Citation Managers that automate PDF ingest and organization