Reference management softwares
JabRef is a java - OS independent - free software. It works directly with .bib files and allows one to search, sort, manipulate bibitems in an efficient way. You can download refs from arXiv by providing the numbers or directly copy-paste bibitems from webpages.
More reference management softwares can be found on the net.
An other possibility, non-open-source, and now own by Elsevier, but still free, is Mendeley. It allows to manage the bibliography (.bib files) and in the same time, to manage, annotate and highlight .pdf files. It can get all the metadata of pdf from the doi or arXiv Id quite efficiently.