I used to use zotero for reference management, but now I use paperpile since it is a bit more stable. One peculiarity of paperpile is that it only provides plug-in for google docs (an advantage in my opinion) since it is easier to collaborate over google docs.
I often encounter having to insert references from a formatted paper in some document format like ms word where the original dynamic references inserted by a reference manager was lost. Doing this manually is very tedious.
There is a work around for this that worked very well when I used it:
Sign up for crossref: http://www.crossref.org/SimpleTextQuery/
and paste the reference list in the window of the crossref site, which returns nicely formatted references.
Then I ran makebib http://www.snowelm.com/~t/doc/tips/makebib.perl.cgi
on the output and uploaded the resulting bibtex file to Paperpile.
Very easy!
