So many references, so little time - and so many choices of reference management tools! What to do?
Today references (also called citations) are not just books and journal articles. They can include websites, data,e-publications, videos and more. Using a reference management tool will make it a lot easier for you to not only collect and store your items, but also to organize and tag them (add metadata) and even save PDFs. A good tool will also provide you with the correct format for citing references in your papers.
It's important to remember that you don't have to wed yourself to any one tool! They each have pros and cons, and you can use different ones for different things. You can usually also exchange references between tools quite easily, so if you start using one tool and decide to move to a different one, you can transfer all your references and not have to go out and find them again.
There are various ways to store PDFs, and you can certainly make use of more than one method. EndNote, for instance, lets you attach PDFs and keep them on your hard drive. The drawback is that they are on your hard drive, and if you are away from your own machine you don't have the articles at your fingertips. RefWorks lets you store PDFs as attachments, and since it's all online you can get them anywhere you have Internet access. The drawback is that you have limited storage, though it's generous. Mendeley (see tab) also lets you store a limited number of PDFs.
In the end, your choice may be dictated by the researchers with whom you work. But that doesn't mean you shouldn't start collecting and organizing references and PDFs in the meantime. This guide, targeted to biologists, will give you a brief overview of the different tools and help you get started.
There is a large and growing number of software tools, free and otherwise, to help you manage your citations. There is no reason why you should choose just one; each has strengths and also weaknesses. You might like one tool for quickly uploading PDFs of articles you want to keep, another for managing and organizing your references, another for wiriting papers. Play around until you find a system - or systems - that you like and are comfortable using. And you can always change, exporting between different tools.
This list is not exhaustive!
There are a number of comparison charts available that give information about the various tools, what they do and what their advantages/disadvantages are. The Harvard guide has one: http://guides.library.harvard.edu/cite/compare.
Wikipedia has a VERY comprehensive list: http://en.wikipedia.org/wiki/Comparison_of_reference_management_software.
If that seems a little overwhelming, Mendeley has one that compares it (favorably, of course) to the other major tools (EndNote, RefWorks, Zotero and Papers):http://www.mendeley.com/compare-mendeley.
Note that these charts give pricing for RefWorks, but it is actually FREE for all Harvard users.