Convert a document's works cited to bibtex or endnote formats

You are spoilt for choice. Google for "reference metadata extraction" and start clicking.

There's free software to extract from PDFs: see Metadata Extraction Tool.

If you have a Word 2007 file, that has (at last) a standardised representation of reflist entries, and EndNote can extract reliably from it.

If you just want to see the citations in an article, RefRuns is a useful tool, and has a simple web interface.

After downloading the Metadata Extraction Tool, I discovered it captures the metadata a of particular object (file name, size, date, etc.); it does not look at the references inside that object and extract them.

The best solution I've found for scraping references from Word and Pdf files is cb2Bib.

You may try WordToBibTeX.

I used it once to convert my old Word bibliography file to BibTeX. :)

The usual path of the word xml bibliography file is something like: C:\Documents and Settings\<username>\Application Data\Microsoft\Bibliography\Sources.xml