These are tools that I find useful in my own work or research. This section is intended mostly to provide a quick list of ideas to new students as they begin thinking about what might aid them in their studies. I will continue adding tools here as I encounter them and / or find them useful in my own work. Please note that all trademarks and copyrights for the included products are owned by the respective companies.
Endnote is my primary reference manager. It allows me to store and retrieve academic references, link PDFs to the reference when I have them, and insert both references and an APA formatted bibliography into my word documents as needed. I highly recommend using it early, regularly, and with notes / annotations so that you have everything in one place from the beginning.
I recently discovered (as in: a colleague suggested this to me) the freeware app Skim for the mac. This is a great little tool for taking notes within a PDF file that I find much much more usable than acrobat pro. Also, the notes are stored in the file-system, not in the actual PDF so that you can then email the pdf to a colleague or student without the notes. It supports attaching notes, highlighting, circling / labeling, a presentation mode, and a host of other handy little tricks.