I'm in the situation where I've installed the JDK, but I can't run applets in browsers (I may not have installed the JRE).
However, when I install the JRE, it clobbers my JDK as the default runtime. This breaks pretty much everything (eclipse, ant) - as they require a server JVM.
There's no JAVA_HOME system property these days - it just seems to use some registry magic (setting the system path is of no use either). Previously, I've just uninstalled the JRE after I've used it to restore the JDK. This time I want to fix it properly.
This also manifests itself with the jre autoupdater - once upon a time, I had a working setup with the JDK and JRE, but it updated and bust everything.