I have been working on whipping my collection into shape for Calibre. I found an awesome application called "Book Sorter" that corrects the firstname/lastname ordering.
http://iterati.org/ebookTools/BookSorter/Default.aspx
It has some other cool features other than renaming and sorting books. It can create copies of your books sorted into genre directories based on the author. I have not experimented with that yet personally though. I used it to fix my collections lastname/firstname issues and it did the job admirably.