I will focus here on only 1 aspect---library organization:
Use bibtex and .bib files. True, but one needs an efficient way to produce them---I recommend zotero (or any other similar program) to organize the library.
This has an added benefit of efficient full text search through all articles that you are using.
In order to synchronize PDF files in the zotero library among different computers, use Dropbox.
Furthermore, I have a perl script (
bibtexformat) to clean up .bib files and make journal name abbreviations.