I would always hand-code the GUI design where there is no standard (or de-facto standard) GUI markup language (as with Java). The reason for this is that I have found that usin a GUI builder design tool will tie you in to using a particular IDE. Over time, the best IDE for GUI design and/or writing code will change and each developer should be free to choose whichever IDE they feel most comfortable with.
Where I work at the moment, we have a lot of legacy GUIs which were written using Netbeans Matisse GUI builder (against my advice at the time :-). These are now almost unmaintainable because all of the developers prefer either IntelliJ IDEA or Eclipse as their IDE. It is not realistsic or workable to have developers fire up Netbeans just to modify GUI layout (people don't keep the Netbeans project definitions in sync etc).
Another point is that the total time writing out GUI layout code is probably only 5% of the total development effort of a given project. Even if it takes you twice as long to write the code yourself, this doesn't translate as much of an overhead in the grand scheme of things. And it's a small price to pay for long-term maintainability.
As long as you are clear about separating out GUI layout logic from business logic, I don't believe anything suffers as a result. No-one here uses GUI builders any more!
