I was just informed, by Secunia Personal Software Inspector, that Sun Java JRE 1.4x (which appears to be part of the Arduino-0012 software delivery) has lots of security problems.
Should the delivery be made with a newer/better-patched version of Java?
Is there an easy way to swap a new Java in, or remove the delivered Java?
If you're on Windows and delete the Java folder that comes with Arduino, it should use one installed elsewhere on your computer. Or try using the run.bat file editing the JAVA_HOME variable inside it.