Hey diebitter,
I'm a Flash designer and programmer, and there are many times when Flash is completely appropriate for an entire site. Most of the sites I worked on were for upcoming movies, personal websites for music artists, or just informational and entertaining sites for major brands.
Obviously, e-commerce sites are not ideal in Flash unless they're using a good company to build it so it works great, but saying that Flash for an entire site is bad is not true. Adobe recently purchased Flash and is stepping it up with every release. More and more sites will be fully made in Flash. It sucks that some companies have low budgets and let crap Flash work slide because it is all they can afford, but I believe they are in the minority.
You can see a lot of good examples of Flash sites at
THE FWA. I reccomend checking out Eminem's and Beck's sites.