The basic metaphors are still the same because we're still using mouses on the desktop. With mobile devices these metaphors break down fairly quickly, though.
HTML-based applications however also introduced a number of new metaphors and patterns such as the page paradigm that, while originally reminiscent of printed pages, is different from anything both in the physical world and within native desktop applications.
Typography and information hierarchy are other aspects that usually can't be implemented as easily or as flexibly with native UI kits as with HTML-based approaches.
HTML-based applications however also introduced a number of new metaphors and patterns such as the page paradigm that, while originally reminiscent of printed pages, is different from anything both in the physical world and within native desktop applications.
Typography and information hierarchy are other aspects that usually can't be implemented as easily or as flexibly with native UI kits as with HTML-based approaches.