I work with a lot of email lists, and constantly have a difficult time filtering out duplicates from two lists. The system we use will remove duplicates on an import, but has no method of removing addresses in an existing list from a new list. (does that make sense?)
Often what we end up doing is pulling them into Excel (or your favorite spreadsheet program) and trying to sort out the dupes there, but it’s a little tricky.
Recently, found this great tutorial, from Microsoft no less, that explains exactly how to do it.