It's very easy you just need to set JAVA_HOME to the output of the command, which should provide you the Java path defined in your Java preferences. Here's a snippet from .bashrc file, which initiates this variable:
I haven't experienced any problems with this technique.
Sometimes you need to alter the value of JAVA_HOME to an earlier version of Java. For instance, one program I'm having requires 32-bit Java 5 on OS X, so while using that program, I set JAVA_HOME by running:
export JAVA_HOME=$(/usr/libexec/java_home -v 1.5)
For those of you who don't hold java_home in your path figure it like this.
sudo ln -s /System/Library/Frameworks/JavaVM.framework/Versions/Current/Commands/java_home /usr/libexec/java_home