I installed 6.9 and imported my settings from 6.8.
Then I used Tools/Servers to remove tomcat 6.0.20 to be sure that no stale references are hanging around when I uninstall NetBeans 6.8 and tomcat 6.0.20.

tomcat 6.0.20 is no longer visible in Tools/Servers but it wasn't removed from my web projects! Instead all of them had an empty choice in Project Properties/Run/Server. I didn't know that and tried to start my main project. That lead to a lot of error messages because my ordinary user couldn't write into the tomcat installation directory. After setting the server for the project manually to the current tomcat 6.0.26 the user writable ~/.netbeans/6.9/apache-tomcat-6.0.26_base/ was created. The project runs now, but there is still the possibility to select the empty entry in Project Properties/Run/Server.

I remember that older versions of the IDE displayed a exclamation mark on the project icon together with a Resolve Server Problem menu item in the context menu.

NetBeans also complains about missing write permissions for the Glassfish installation directory. I fact I never used Glassfish for my projects. I only installed it together with the IDE.