Here is the link to install the application (Note that you must use Internet Explorer for this installation process). Before you install you need to make an empty folder in your C: drive called "export" (without the quotes). The installer will not function properly if you don't do that first.
Once you have made the export folder, open this link in IE http://apps.library.yale.edu/CompareData/publish.htm and click on Install. It will take a minute and you'll see a "verifying..." window while it's working. When the install is finished the app will launch. In the future you can launch it from the Start Menu Programs List under Yale University Library.
The app is quite simple and intuitive - you simply load your two lists as text files using the Load File 1 and Load File 2 buttons. You'll see the lists appear as you load them just below the buttons along with a row count. In the boxes below your lists you'll see any duplicates that have been found in the individual lists. In the first box to the right you'll see any items from File 1 that are not in File 2 and in the furthest right-hand box you'll see any items from File 2 that don't appear in File 1. All of those lists can be exported as a text file with the associated Export button which opens the list in Notetab.