This is a question which has often come up on the webz.
I am not really sure of your exact requirements but Mendeley has some of the functions or you could develop a workaround. See this and this. I have also heard good things about Sente but I have not used it.
These are solutions for Macs though. I am not sure about Windows and do not know if that is a constraint which you have. Personally, I use a hierarchical folder system in Mendeley and export to BibTeX and add tags - which, so far, seems to work well enough.
Are you seeking more, in general of optimizing your academic workflow? In case you haven't heard of it, I suggest visiting this blog. It updates sporadically but most of the good stuff is in there. I hope this helps.