If you are using Java Swing to build your GUI, you should be using jGoodies Looks (SWT-like clean Java Look & Feel library), Forms (layout library), and Animation (animation framework). They are free, open source, and, best of all, great looking. When I say great looking, I mean Audrey Hepburn good looking: clean, crisp, and neat.
I have yet to see a better way to minimize the mess most Java programmers call GUI. If a stray pixel doesn't bother you like a thorn does, you need jGoodies badly. jGoodies is also a member of java.net's JavaDesktop community. Go check it out.