Hi!
In medicine (or an area where many of your articles are indexed in PubMed) we have a way of generating an EndNote import from the reference list of a Word or pdf document by using a service called HubMed Citation Finder:
http://www.hubmed.org/citation.htm
I have made a guide for this, but it is in Norwegian only (hopefully you can use the figures to understand):
The short version: You copy references from a reference list into HubMed Citation Finder, which will try to find the references in PubMed (this will not work if the reference is missing from PubMed or the reference is not an article). NB! One problem is that HubMed will report that it has found some references that is not the one originally in the reference list!! It is therefor important to check the list HubMed generates thoroughly. The resulting HubMed list can be be imported into EndNote using the RefMan import filter.
This is not a perfect methods (I have gotten a 75% sucess rate in my tests). Also note that the imported references in your library from this methods will not get the same EndNote numbers as they had originally in the manuscript and you will probably will have to go through several Select matching reference error messages to fix this in the manuscript. An alternative is to make a copy of the manuscript, remove the EndNote field codes and insert all references again from the restored library.
If you are not working in the medicine/health area, this info will probably not help you. I do not know if there are similar services available on the net for other research areas.
Best wishes
Jan Ove