This paper further develops the concept of an applied geographic information system (AGIS) for modeling search correlation-extreme navigation systems (CENSs) intended to control moving objects. The possibility of using parallel, distributed, and cloud computing for modeling CENSs is investigated. In modern conditions, it is necessary to diagnose the operation of CENSs under stress exposure on their shooting systems. The stress exposure parameters are modeled by accessing specialized databases containing the characteristics of terrain objects in different electromagnetic radiation wavelength ranges. As a rule, such characteristics are unavailable in geographic information systems (GISs) and cloud environments. It is demonstrated that CENSs should be diagnosed by modeling the shooting system using cloud GISs. The issues of parallel computing for pattern recognition tasks are considered. The peculiarities of the parallel structure of CENS search algorithms are revealed. When implementing these algorithms in parallel computing systems, proper consideration of the peculiarities allows utilizing their advantages to the highest degree.