I would put it down to there finally being a distinction between web-sites and web-apps.
Within an app, my current context (which control has the focus etc) is important and a full page reload loses all of that.
Within a web site, as it is less interactive, this stuff doesn't matter so much.
As to whether New Twitter is a site or an app is debatable (I say site and therefore shouldn't be using #!). And as for Gawker...
On many examples I don't see any real disruption to application flow with just using normal links, though there are more full-fledged webapps (like gmail) where I would agree. Playing around with old v. new Twitter, the old one actually has considerably faster navigation performance, at least on my setup (and I'm using a recent Chrome on a recent Macbook Pro). Sure, some HTML header/footer stuff is being retransmitted, but it's not very big.