An efficient technique for saving your Internet Explorer favorites is to use the "Import and Export" option from the File dropdown menu. It results in a default file "bookmark.htm" containing all of your favorites and preserves any folder structure you may have established.
To transport them to another desktop, first delete all the "Favorites" folder contents on that machine (under "C:Documents and Settings <userid>"). Then launch Internet Explorer and use the "Import and Export" feature to import the saved favorites from the export file "bookmark.htm." All the favorites will be restored on the target machine.
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