Being a few months into my PhD, I think the biggest shock I've had is dealing with the vast quantities of information that suddenly seem to have appeared in my life. In the last few weeks this reached a crisis point, and I have been making a proper, grown-up effort to get everything in order before I drown in a bibliographic swamp.
One piece of software that has intrigued me, and which seems to be fairly useful is Mendeley, which describes itself as "i-tunes for research papers". Given how irritated I got with i-tunes, I suspect this doesn't do it justice (plus you don't need to give Apple your credit card details to get anything done).
Mendeley is currently in beta, and so is a little bit buggy. It wants to be a bibliographic tool, but I'm not using it for this, at least not until it gets slicker. What it does do incredibly well is to centralise pdf documents and allow you to order, search and annotate them. Plus its free!
Previously, all the papers I was merrily downloading were ending up in a series of folders, somewhere in the depths of my laptop. The more I added, the scarier and less accessible they got, and the more helpless I felt. With Mendeley, I have organised them into folders, and some papers are in a number of different folders, because they cross subjects.
Mendeley works by "watching" particular folders, and then bringing new papers up when you open it. Again, this is a little bit buggy at the moment, but better than the alternatives (madness, depression, alcoholism...). The main irritation is that it sometimes ends up bringing multiple copies, but this is fairly quick to tidy up.
Here are some screen shots:
Here is the list of all my papers. You can also see the folders I've created down the left hand side, and the info on each paper on the right, which can also be edited, or checked via google scholar (which I also love).
Once you've opened a paper, you can highlight and annotate it...
You can also search for key words in all your papers...
It doesn't currently work for anything other than pdfs, but what I have done is turn some of my typed-up notes into pdfs, and then added them too.
All of this does take a bit of time to set up, but seems to be worth it once it's done. Given that I've only been using it for a few weeks, I would be really interested to know if anyone has had any good or bad experiences of it themselves.
And if you're currently wading through a mire of academic papers, you could try taking the road to Mendeley (now I have Nellie the Elephant in my head... "trump, trump, trump!").