Any pilot with the requisite hours can apply to the C-9. It is competitive by board selection. It is a career killer, but a lot of majors and ltcols try to get it as a farewell tour, since it is definitely a source of quality flt hours for outside employment.
The other fleet support aircraft, such as the C12,20,and 35 are assigned by the monitors. Any pilot can try to get these slots. Again, they aren't good for your career, but they are pretty highly coveted for the multi time they put in logbooks.