You can put an aftermarket headunit in a Prius. Its just more complicated. You might want to go to http://www.greenhybrid.com/discuss and ask around on the prius forum for the details. They can tell you exactly what you can and can't do.
Its also a good site for you anyway if you are getting a hybrid.
My understanding is that the prius isn't too different, so most things you can do to a regular car you can do to it.