I imagine you are making a distinction between the metadata and the content of the file, correct? I imagine that this will be difficult to do since the metadata is part of the file. One possible route would be to investigate how SharePoint generates the notes that it includes in the version history. You might be able to use Reflector to look at the SharePoint assemblies to get some clues. Another option would be to open both files on the server with COM Automation (for example if they were word files) and compare the metadata that way.
good luck --
John Azzolina
www.johnazzolina.com