PDF and citation collections can get overwhelming very quickly. Mendeley is a great tool (and free!) to use to keep your reprint library organized. It’s somewhat like Endnote if you are familiar with that, but has some other really great features. I guess I should admit I haven’t used Endnote in a long time, so they might have caught up and added such features.
My favorite feature of Mendeley is that it can “watch” a particular folder for any new additions. So, if you have a folder of pdfs, it will automatically add a new pdf to your Mendeley library. Also, if that pdf is relatively “new”, it can use the file’s metadata and fill in all the important info fields automagically. Info fields like Title, Authors, Pages, Abstract, etc. For old pdfs, or ones you have scanned in yourself, you can either type those fields in manually, or used Mendeley’s “Search by Title” option, and it will search on Google Scholar for the paper, locate it’s metadata, and fill in all the info fields automatically. I find that I rarely have to go in and enter info fields manually.
Making groups of papers by topic is a cinch. If you want to locate papers relevant to particular topic quickly, you don’t need to make a separate folder on your hard disk. Mendeley will create its own folder, and the original location of those papers doesn’t on your hard disk.
There are many other great features to Mendeley, which are also free, but if you want to give Mendeley money they will give you space in the cloud that allows you to access your reprint library wherever there an internet connection. They do give you a modest amount of space for free (500mb I think). But for $5 a month, I think it goes up to 5 gig.
Check it out if you haven’t yet. I’ve found it to be very useful.