I use JabRef (Java based open source tool, jabref.sf.net) which stores references in BibTex - suitable for my preferred authoring environment LaTeX, but allows import/export in numerous formats for when I'm writing with Word templates. JabRef allows you to create quotations as part of the bibliographic record, and has a very effective search mechanism. There are many styles for presenting a BibTeX based bibliography, including APA, MLA and others. JabRef also allows for multiple URLs for the same resource: typically I print to full text PDF and store locally with a URI, plus reference the remote source. For my local copy, I use Terrier (http://ir.dcs.gla.ac.uk/terrier/) as the search tool (unerstands binary formats like doc, pdf). YMMV. baden