Two of my company's three products are a Java desktop app for Mac, and they look and feel like typical Mac apps.
Best practice? IMO you should spend significant time on the GUI making sure it feels native. Otherwise, Swing is still about as good as it gets for Java GUIs. JavaFX is supposed to be more modern and superior, but lacks the large-scale support and third-party component ecosystem that you find the Swing. Although I'd be mighty pleased to be proved wrong on that one!
I've never seen any Java desktop app that I cannot easily tell it's Java. With most of those apps, even on i7/16GB/SSD systems, you get laggy behavior with Swing and the GC. And SWT still has the "uncanny valley" look going.
It took several seconds of whited-out buttons and stuck UI for every CPU intensive operation -- all on the same thread. And that was from IBM, and from tools that you paid for a small fortune.
I'd also venture to say a lot more than 1%. Modern world (finally) recognizes that design/experience are core to any product, enterprise or not. That's part of the reason there's a whole new breed of funded enterprise companies out there -- they're taking lessons from the web/apps and applying them to replace old-school solutions. [I'm personally hoping more people recognize this need for developer tools which typically are the worst offenders of all, particularly on the database side.]
Part of having a good framework is what allows apps/applications to excel -- it helps you raise your own bar because the tools are just so much better that nicer UI/UX can be had without being a nightmare in code. That's a win for everyone.
More seriously, as a recent example you will find that what bitcoin.org offers you as the first option for a wallet (multibit) is written in java.
That may not be mainstream, but it's definitely not the classic enterprise java shop.
I've been writing UI code for years, including in Java, .NET, Android/iOS, web, etc, so I have a pretty decent clue about building complex apps in all of these frameworks. Java just isn't a modern environment, and by being cross-platform you end up with an ugly lower common denominator that doesn't have useful APIs for non-trivial designs. iOS is probably the best framework/api out there and even that has many issues (luckily obj-c's categories help you fill in the holes).