Eclipse is using the wrong vm for me under Gutsy:
$ eclipse
searching for compatible vm...
  testing /usr/lib/jvm/java-gcj...found

$ sudo update-alternatives --config javac
There is only 1 program which provides javac
(/usr/lib/jvm/java-6-sun/bin/javac). Nothing to configure.

$ sudo update-alternatives --config java
There are 4 alternatives which provide `java'.
  Selection    Alternative
-----------------------------------------------
*         1    /usr/lib/jvm/java-6-sun/jre/bin/java
          2    /usr/bin/gij-4.1
          3    /usr/bin/gij-4.2
 +        4    /usr/lib/jvm/java-gcj/jre/bin/java

$ dpkg --list eclipse
ii  eclipse                           3.2.2-3ubuntu3                    
Extensible Tool Platform and Java IDE

$ dpkg --list 'sun-java6-bin'
ii  sun-java6-bin                     6-03-0ubuntu2                     Sun 
Java(TM) Runtime Environment (JRE) 6 (architecture dependent files)

I am currently working around this by invoking from the command-line:
$ eclipse -vm /usr/lib/jvm/java-6-sun/jre/bin/java

-- 
Package eclipse does not work with Sun Java 6
https://bugs.launchpad.net/bugs/132645
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Bugs, which is the bug contact for Ubuntu.

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