When you are using Ubuntu and upgraded from older releases to intrepid or jaunty you might have run into a setup bug which causes the browser to keep using the old java plugin despite having latest Java SE and plugin packages installed (e.g 1.6 update 13 from multiverse repository).
To fix this you will have to update some symlinks and let them point to the correct location.
one easy way of doing this is by using the update-alternatives command:
sudo update-alternatives --all
this will iterate through all symlinks in /etc/alternatives which have more than one alternative and ask you which one to use. Simple update all links which point to:
to the location of the new plugin (e.g for i386):
For all other links just hit Return.
This is a little bit of a brute force approach but there shouldn't be many of them and it is the only way to make sure you don't overlook one of them since they are all called differently ;)
Next time you restart your browser the new plugin should be loaded
and applets which use e.g jnlp for deployment (or out of process functionality) should work.