I typically refer to any assets on my site using absolute path so that I don\'t have to worry about the location of the assets relative to current file.
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what about using html's BASE element? http://www.w3.org/TR/html4/struct/links.html#h-12.4
although i´m not sure how you could have it in a single html file and inherit it to the rest of your htmls, so your source remains intact. if your site is html-only maybe with frames, otherwise you could use some sort of server-side include depending on what youre using (asp, jsp, whatever). Check out this link for more information http://www.boutell.com/newfaq/creating/include.html