Well, I haven't had any problems.
I installed java using synaptic. It's the sun-java6-jdk package.
This works out of the box, with eclipse, the command line, etc.
If you unzipped the jdk, then
http://www.cyberciti.biz/faq/linux-unix ... -variable/
shows you how to set java_home. I'm sure it's available from SUN, too.