Maybe you've got a clothing e-commerce site, and you just cleared out your summer fashions.
Maybe you've got a travel agency and you're deleting the 2008 tour descriptions, cruise itineraries, etc. to make way for the 2009 offerings.
Maybe you run a university site, and you've replaced all of the 2007-2008 course descriptions with new pages for 2008-2009.
Or maybe you just redesigned your site and cleared out a lot of clutter.
In short, there could be any number of good reasons why a "quality site" might have major (and sudden) page turnover. And by using a 404 instead of a redirect to the home page, you're simply sending a signal that the pages are gone--you aren't doing anything that looks even remotely deceptive.