sigh Never touch a running system.
However, should you touch it, here is the quick pain relief for Java applications under Intrepid Ibex (aka Ubuntu 8.10). To be honest, I don't know if that is for Java applications in general or just for the specific one I really do use:
JabRef. After installing Xubuntu (or Ubuntu and the standard Java Runtime Environment) the program looks like this (click for the whole pain):
That sucks. It only took me 3 hours searching the web (with no real result, actually, seems like that is not a common problem) to finally fix this. This is how it is has to look like (click for the relief):
The difference? The upper one is with the openjdk-6-jre that seems to be the 'preferred' choice as the Java environment for Ibex. The correct, lower one is with sun-java6-jre. And the really annoying thing is: I installed the proper Sun Java stuff right after installing the system, operating under the illusions that it will actually get used.
*Bah*. I certainly have better things to do at the moment.