When moving to a paperless workflow, there are digital solutions that can help preserve the organizational structure you are accustomed to using for paper documents, and can take the place of hand-written marginalia.
Adobe 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 can be used both by individual users and in a collaborative environment in which multiple users can comment upon a shared PDF, similar to the "Track Changes" feature in Microsoft Word.
There are also many free or low-cost alternatives to Adobe Acrobat Professional which provide organizational or editing features.
PDF software available for Windows includes:
- PDF X-Change Viewer, a free PDF editor
- FoxIt Reader, a free PDF reader and annotation tool
- PDFill, a low-cost PDF editor with numerous tools for marking-up a document
- PDFMerge, a free tool for combining multiple PDF files
PDF software available for Mac includes:
- Preview, a PDF reader included with Mac OS X, able to merge and add notes to PDF files
- Skim, a free PDF manager intended to help with reading and annotating scientific papers
- Papers, a low-cost document manager designed for locating and collecting scientific articles
A substantial list of additional PDF software is maintained on Wikipedia.