I am running Eclipse Helios SR2 (the EE version) on Ubuntu 11.04. 
I installed tomcat6.0.29 manually and can start/ stop it ok.
I can add the Tomcat 6 Server Runtime environment successfully to eclipse - I've never had the "Cannot create the server" problem however the environment **never** show up in my Servers view.

I've tried many avenues but no success (same issue with installing the aptitude tomcat6 and creating links etc)
Any suggestions on how to progress this ?

Other info:I have exactly the same issue with a brand new install of Eclipse Indigo (the EE version)

I have java-6-sun installed:

update-java-alternatives -l
java-1.5.0-sun 53 /usr/lib/jvm/java-1.5.0-sun
java-6-sun 63 /usr/lib/jvm/java-6-sun