CCF comes in pretty much any design you like, thanks to having the source code for the agent desktop available. One of the properties of the applications you add is a "Display Group" property which allows you to set where you want the application to go. If you leave it blank, then it defaults to the first CCF panel it finds. If you fill it in and it matches the name of an existing panel it will go on that panel (have a look at the out of box examples for Workflow, Current Session and Session Explorer).
not documented anywhereUpdated: It is in the developer guide is you can also put in either "floating" or "floatingtool" which will cause the window not to be in the CCF SDI interface (i.e. on the tabs or on some other area) but in it's own pop-up window. The "floatingtool" option changes the type of pop-up form to a tool form (i.e. thin header).
it is possible to push the boundry on this one further by putting in your own terms, and then modifing the "AddApplication" method of UIConfiguration.cs to handle those special terms. An idea I had here is that you could do something like have the window be stay on top, align to the right of the window and have it load a reporting services report with graphs on it. Nice mini-dashboard!