Java apps done right on Mac OS X look, feel and behave like actual Mac OS X applications, Cyberduck is a free FTP client written in Java for Mac OS X. It is a great example of what is possible in Java.
But there are plenty of apps out there that are mere ports (Qt, or Java) and you can feel it. The drag handles are in the wrong location, the app doesn't behave right when you resize it, the buttons are in the wrong place, or switched from where they are supposed to be. I will still use it, but if something "native" comes along I will switch to it in a heart beat.
First, I disagree that well-done Java apps on OS X actually hold up as OS X applications. It is as Alex says; there's an uncanny valley, and Java apps fall right into it. Cyberduck is as good as it gets, and, compare it to Panic's Transmit.
Second, if you've seen Bingo Card Creator, you know that his users weren't buying it for its elegant OS X-ish interface.
I've used Cyberduck for years, I'm a fairly technical person, I care about native apps... and yet I never realised that Cyberduck was written in Java.
So they've done a pretty amazing job. Perhaps that's possible in AIR too, but I don't know of any such apps (then again, I didn't know of any such Java apps until a moment ago).
Yes, that's a great example. If you sat me down in front of the two, I could not easily tell you which was the Objective-C application and which was Java. I used Cyberduck on an almost daily basis for years without ever realizing it was Java. That is the app that convinced me Java has a place on Mac OS X.
That's because Cyberduck calls the native Cocoa Objective-C APIs[1]. This is doable, but it's a lot of work and won't run on anything other than OS X. Something cross platform that uses Swing won't feel as nice. Also, it uses a third party binding to the Cocoa libraries. Apple deprecated theirs quite some time ago.
I have used Transmit and found it to be less easy to use than Cyberduck, that and I am cheap, I used to pirate software, since I switched to Mac OS X entirely at the beginning of my college career I refuse to pirate software that runs on my Mac.
But there are plenty of apps out there that are mere ports (Qt, or Java) and you can feel it. The drag handles are in the wrong location, the app doesn't behave right when you resize it, the buttons are in the wrong place, or switched from where they are supposed to be. I will still use it, but if something "native" comes along I will switch to it in a heart beat.