The best solution I've ever seen that doesn't quite get as granular as
you are hoping for changing _layouts for a separate Web Application.
(_layouts is typically static across an entire WFE and Farm).

You can copy the contents of the LAYOUTS folder and create a separate
web application which has an IIS virtual directory of _layouts pointed
to the different location. You can put your customizations there.

Some other things I can think of would be to create a new applications
master page. You could then maybe subclass the publishing bar, or write
a custom RenderingTemplate if it utilizes _controltemplates/*.ascx.
Maybe you could create a control that if some parameter exists, it would
use your custom control and if there were no parameter it would display
the default control.

Remember SharePoint is extremely customizable as long as you are willing
to take it like it is.

Thanks - that'a a great approach that I would never have thought of.

Tell me how it goes. I have some brave ideas but not the coding skills
to back it up!