This PPT presentation (5.5MB) explains what EZGov (a company building e-govermnent applications) does with Visio and VBA macros. This app is internal only for now (though the team is considering turning it into a product), but the idea is interesting anwyay.

The trend is definitely towards mockups that feel like sites, though you can't really afford that luxury on smaller projects with current tools (for the poor or hurried, hyperlinks within Powerpoint documents are better than nothing). Ideally software should let us re-use work done at the prototyping stage (think web RAD), but actual code and design generation out of Visio or Powerpoint documents is not going to happen soon (though that's propably a very bad idea anyway except for micro-sites). There's, however, Visio support in Visual Studio Enterprise Architect to generate database models and business rules.