[capink]

Calibre does actually provide the feature you are asking for. Open the first book in calibre editor, go to file > compare to another book > choose the book you want to compare against.

Edit: Note however that feature probably only going to work for different revisions of the book, by the same publisher. If you have to different copies for the same book published by different publishers, the xhtml filenames are probably different and I don't think the comparison would be of value in this case. Never tried this myself, so you have to test it yourself.