i'm also stuck on this.
- installed java-5
- installed eclipse
-> eclipse ran fine
- installed java-6
- uninstalled java-5
-> eclipse from the menu gives: The custom VM you have chosen is not a valid 
executable.
- uninstalled completely/reinstalled eclipse
-> same problem

eclipse from the command line is fine w/ and w/o JAVA_HOME

-- 
[Reopened] [Dapper] Eclipse startup script should respect jwm setting via 
update-alternatives
https://bugs.launchpad.net/bugs/36534
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