
I don't think it's too hard to get a completely standardized Java running on Linux. When I installed Ubuntu, I got OpenJDK, but I'm not sure I like that very much; it seems like a weird mix of Sun's open source Java and a lot of goofy stuff from the FSF, like their Classpath project.
What I do is create a Java directory in /opt, download the REAL JDK from Sun, install it to my new /opt directory, and adjust my profile file so the bin directories of the JDK and the JRE come first in my PATH. Then I specify CLASSPATH wherever I need to, and target the official JDK in my tools, like NetBeans.
Problem solved: I'm using the canonical Sun-provided version of Java, and the weirdo OpenJDK Ubuntu likes to install gets ignored.
Sorry if this offends any of the OpenJDK folks... You lost me when you decided to replace the binary stubs in OpenJDK with GNU Classpath. You should have re-implemented the missing code from scratch, cleanly, instead of building a big, clunky Rube Goldberg contraption out of two separate systems.
You Unix beards always try to glue everything together from a million tiny programs... You even call it "The Unix Way". For scripting projects, that's fine, but for a large, complex project like a JDK??? Yuck. Rube Freakin' Goldberg.