Comment Re:Zotero (Score 1) 211
I'll second Zotero as well. I also use Zotero (I'm also a doctoral student and use it to handle my research). As for copying between computers, I've never had a problem. I just set it up to store everything under a specific folder rather than the default one under the Firefox profile, and copy that folder between computers.
As for citation formats, I did have a few problems until I figured the easiest thing to do was to leave everything as defaults. I was exporting to Bibtex format and importing it into LyX and wanting to change the style slightly. I could have created a zotero xml based export style but it was easier to leave it as was as all I wanted was a small change to the default one.
That brings up the one thing I would like changed/added: use or import normal Bibtex and/or Endnote styles rather than creating another way of doing the same thing.
There may be another solution that fits your needs if all you want is to keep track of a lot of files but if you also make notes on them, tag them, and say which is related to which, and even create snapshots of webpages etc. its just great. I'm also using it as a simple store for various piles of open source code I may want to find, use, or refer to later.