OK i got so far as to edit the ONET file ( I did make a copy of it first :-> ) to add the code that jonathon frost used in
http://www.jjfblog.com/2006/12/one-issue-that-came-up-during-recent.html
This works for the Document Librabries, but what about content query web parts, that does not work. Has anyone found a solution to opening documents in new windows across all sites and pages.