I'm yet to inherit a PHP project that does not contain a file called "functions.php" and it always makes my heart sink when I see it. What I don't get is the demand for all kinds of stuff to be built on top of wordpress that doesn't really have much to do with content management or blogging. For example online games, CRM systems, auction sites etc. Seems a bit like asking for a CMS system that has been implemented as…
Consider an online business directory. You could just build one from scratch or use some script designed for that purpose but WP simply offers more flexibility. If you decide you want a Google Map displayed in each listing, just download the relevant plugin. If you want to add oEmbed functionality (for, let's say, embedded videos), it's already built-in. If you want to do advance taxonomy queries use the Taxonomy Drill-Down plugin, etc.
Yes, it's all held together with chewing gum, but it works.