That's because they're using Javascript to render a lot of stuff. iOS doesn't support position:fixed, doesn't support div scrolling (although I think this is being fixed in iOS5) so the common thing to do is to hack together a javascript shim.

I think that's the wrong approach. Let the browser do the things it does well. Use javascript to enhance the browsing experience, not to fill holes.

We're undergoing a shift in web design where the purpose is to make web applications look like native applications. I think in a couple of years we'll see a rejection of this and instead have web applications which look like websites but have the capabilities of native applications.

Let scrolling work the way it's worked since the web was created. Instead of hacking a page flip animation, precache the next page. Instead of capturing every click event, use cache.manifest and smart pre-caching to let your app look like a single page app even though it's not.