I use Mendeley to organize and view articles (pdf files). It is almost good, however I wish something similar with one additional feature. A software to make a link for every reference in the Reference section of any article I read (not my own articles) and when I click on the link it searches the web for it, or if it has a downloadable version, directly points to that file and if it is already exists in my articles opens it.
Digital Object Indentifier (DOI) names might be a possible solution. Sometimes article citations in major databases come with them - if so, you can use them to directly access the paper (in a web browser, at least).
For example, for Claude Shannon's seminal work A Mathematical Theory of Communication, the DOI name is 10.1109/9780470544242.ch1. This can be resolved either by using this website, which also describes DOI names in detail; or by using a direct link, such as http://dx.doi.org/10.1109/9780470544242.ch1.
You can find these DOI numbers either by checking reference databases (which often include them) or by checking a website such as crossref.org.
IIRC, Mendeley actually includes a field for the DOI name, if known. I've seen it automatically populated when I use the browser clipping tool (sometimes, not always).