If you could add just a text area that would allow users to inject some javascript code into the agent interface. I'd really like that.
Basically, I want to do what greasemonkey allows... but don't want to have to configure greasemonkey on all my agents computers.
I heavily customized the portal for my end users... but my agent interface is now behind the times. In order for agents to access all the awesome features we've added we can't do so without having two browsers open and logging in as user.
Simple solution:
Add a way for us to inject some javascript on the agent interface. Basically you'd just put the contents of that box before the closing </body> tag.
Then, savy developers could make minor modifications such as hiding useless things from interface with simple jquery hide(). Adding a tab or two to get to the issues we don't like in the interface we could fix
You don't have to make it really complex like like the themes with ability to modify all the page layouts etc... 1 place to inject code would be sufficient.

