If you are using a closed source or commercialware application for referencing, then your archival reference database will be weaker than choosing an open-source alternative.  Anyone who has endured watching a file format (and/or software application) shutdown due to laws that allow any computer company to sell you software then have that software shut down, know what I am talking about.  Examples include Freehand, Hypercard, and Owl Guide.

The strongest open-source alternative that I have found is Zotero (http://www.zotero.org).  A second but less convenient choice is the database feature in LibreOffice (http://www.libreoffice.org.

Zotero has great referencing features blended into a Firefox plugin for MAC and PC.  In addition, plugins exist for Microsoft Word, Open Office, and now LibreOffice.  Given that the Zotero application is stable, open-source, and free - then why is it that when I talk to educators, no one has heard of this software?