Just a quick update about my favorite formats to use!
I've previously posted about the joys of (free, open source, easy to use) OpenOffice Writer over the dreaded (expensive, commercial, horrible) Microsoft Word; and the joys of (free, open source, easy to use) Zotero over the dreaded (expensive, commercial, horrible) Endnote.
However, the .doc format is, however, ubiquitous and if you start passing round .odt people get upset. But you don't need to use Microsoft Word in order to save in Word format! Open Office can save in Microsoft Word format (and PDF, Latex and MediaWiki for that matter)! You can also still use Zotero.
The particular referencing convention I tend to use is Author-Date (Harvard Reference Format 1) which stores the references as Endnotes, and I format using Bookmarks. Bookmarks are the format for use in word documents.
Comments: Zotero has an annoying habit of going back to Reference Marks when you click the set document preferences button. You need to ensure you stay on bookmarks if you do this. Zotero is fairly stable, but occasionally there are problems. It's best to backup your work regularly anyway.