If your documents are properly structured using styles (which is rare)
and they share the same styles (and I mean the *same* styles), you can
try to use openoffice in remote command mode, convert the .doc into
..odt, parse the xml of both files, proceed to merge the XMLs and
rebuild an odt file; perhaps going through OOo again to have a .doc
back. But you will need to ensure that the styles are always converted
into something reliably identifiable.

FAO (the UN branch for food and agriculture) uses a template system
(thus forcing a set of styles) which is used to output RTF which is
converted into XML for storage. Are your documents existing legacy ones
or is this a new setup? If you're building it all, then you might
seriously consider using openoffice all the way.