The only valid case for this (IMO) is really expensive professional apps. Where someone is going to spend years getting really, really good at using a piece of software, and you want them to be able to just use it the same way regardless of platform. And you especially don't want people to have to re-learn how to use your really complicated software if the host OS changes how scroll bars appear or the position of window chrome.

But I suspect lots of software companies would think that describes them, when in reality there's probably fewer than 10 products that meet that bar.