I have struggled to organize my research papers and articles. They are placed in folders within folders within folders. The Apple operating system (Lion or prior) helped with searching documents, but it was never the same.
Recently I started using "Papers" - http://www.mekentosj.com/papers/
Brilliant piece of software - mainly for Apple OS, but they are coming out with a Windows edition too. Works with iPhone and iPad too. All the devices sync with each other. Pretty cool.
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