Creating .bib file containing only the cited references of a bigger .bib file in Windows

If biblatex/biber is an option, you can use biber to generate a document-specific .bib file. All you need is a document using biblatex compiled to generate the usual .bcf which biblatex/biber uses. Then you can run:

biber --output_format=bibtex --output_resolve <filename>.bcf

where <filename> is the name of your <filename>.tex.

If you don't mind installing jabref, it can do it for you. Both command line (link here) and gui options are available. From command line do

jabref.jar -a filename[.aux],newBibFile[.bib]

You should be done. Take care that jabref.jar is in system path, and run this command from the same folder as your .aux file.