Two of the challenges with moving to a paperless workflow are preserving the organizational structure previously established for one’s paper documents, and replacing the easy flexibility of hand-written marginalia. Fortunately, many products exist to help with these challenges.
Adobe’s own Acrobat Professional, available at an academic discount through OIT Software Sales, includes an Organizer to help you manage collections of PDF documents. Acrobat Pro also includes many tools to annotate existing PDFs with arrows, highlighters, sticky notes, and the “typewriter,” which lets you add text directly onto the PDF as if it were a paper form placed in a typewriter. Acrobat Pro is designed to be used both by individual users and in a collaborative environment in which multiple users can comment upon a shared PDF. This functinality is similar to Microsoft Word's Track Changes feature.
There are also many free or low-cost alternatives to Acrobat Professional which provide organizational or editing features. Some of these programs include:
A substantial list of additional PDF software is maintained on Wikipedia.