To organize papers, I use Zotero. https://en.wikipedia.org/wiki/Comparison_of_reference_manage... has a long list of reference management software, some of which have modified PDF readers which allow, for example, user annotations.
To organize papers, I use Zotero. https://en.wikipedia.org/wiki/Comparison_of_reference_manage... has a long list of reference management software, some of which have modified PDF readers which allow, for example, user annotations.