Although I have no personal experience with it, I observe that ASCE 7-05 11.4.7 allows a site-specific ground motion procedure for "any structure." In particular, 21.2 sets forth requirements for obtaining a site-specific MCE response spectrum.
Aside from the cases of seismic isolation or damping systems, as specified in 11.4.7, are there any other situations where you would want a site-specific MCE response spectrum for design rather than relying upon the code-specified response spectrum?