Getting to the bottom of the eclipse case, I'm starting to agree with
earlier posters.

If you specifically drop the JAVA_HOME which the eclipse script has
carefully introspected, and just use the java binary which is available
to you on the default path, leaving the final lines of  /usr/bin/eclipse
as...

unset JAVA_HOME
JAVACMD=java

# Do the actual launch of Eclipse with the selected VM.
exec /usr/lib/eclipse/eclipse \
    -vm "${JAVACMD}" \
    -install "${INSTALL}" \
    -startup "${STARTUP}" \
    ${CMDLINEARGS} \
    -vmargs -Djava.library.path=/usr/lib/jni \
            -Dgnu.gcj.precompiled.db.path=/var/lib/gcj-4.2/classmap.db \
            -Dgnu.gcj.runtime.VMClassLoader.library_control=never \
            -Dosgi.locking=none ${VMARGS}

...the eclipse application seems to load perfectly fine. In other words,
if it simply runs 'java' then it picks up the default version as
determined by update-java-alternatives, and yet it's chosen a byzantine
way to load java, through JAVA_HOME, then generating a java binary
location based on JAVA_HOME.

Using the environment variable approach requires that presumably every
script has to load up with the JAVA_HOME environment variable set, even
though it's entirely irrelevant for most scripts.

If this happens for every application and every dependency, not just
JAVA, but also Corba, IP Networking Gateways and everything else,
because specific environment variables are allowed as an assumption on
the part of loading applications, the tables get very large very quickly
and everything slows down.

Perhaps a concrete recommendation might be that JAVA_HOME in the eclipse
script should get derived from the path of the 'java' binary, rather
than the other way around, then it would be possible for ubuntu to meet
its expectations without throwing environment variables around.

-- 
update-java-alternatives does not change the JAVA_HOME
https://bugs.launchpad.net/bugs/45348
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