Boy, do I feel stupid. As soon as I posted my blog, people pointed out to me that NetBeans 6.0 Beta 2 supports IcedTea out of the box, so all my hackery with NetBeans 5.5 was pointless.
However, NetBeans 6.0 Beta 2 doesn't work for me. It just displays a blank screen. After a little while, I've found out why. I always run all my test programs as X clients on a remote mcahine, with the server running on my desktop machine. It turns out that if you start 6.0 Beta 2 on the same machine as the X server, it displays correctly.
I suppose that NetBeans must be doing some of the same weird stuff that we've seen elsewhere, and trying to bypass part of the X protocol somehow.