Excel should be able to do this.
Depends where the data is.
Quick method of doing this would be creating a smart list with two filters inside it "Member of List 1" "Not a Member of List 2". It will resolve your problem upto some extent. Apart from this, we have our own De-dupe product for account matching and for bigger databases. You can contact us at email@example.com for more information on this. We would be happy to help you!