Linear covariance analysis has been utilized in a wide variety of applications. Historically, the theory has made significant contributions to navigation system design and analysis. More recently, the theory has been extended to capture the combined effect of navigation errors and closed-loop control on the performance of the system. These advancements have made possible rapid analysis and comprehensive trade studies of complicated systems ranging from autonomous rendezvous to vehicle ascent trajectory analysis. Comprehensive trade studies are also needed in the area of gimbaled pointing systems where the information needs are different from previous applications. It is therefore the objective of this research to extend the capabilities of linear covariance theory to analyze the closed-loop navigation and control of a gimbaled pointing system. The extensions developed in this research include modifying the linear covariance equations to accommodate a wider variety of controllers. This enables the analysis of controllers common to gimbaled pointing systems, with internal states and associated dynamics as well as actuator command filtering and auxiliary controller measurements. The second extension is the extraction of power spectral density estimates from information available in linear covariance analysis. This information is especially important to gimbaled pointing systems where not just the variance but also the spectrum of the pointing error impacts the performance. The extended theory is applied to a model of a gimbaled pointing system which includes both flexible and rigid body elements as well as input disturbances, sensor errors, and actuator errors. The results of the analysis are validated by direct comparison to a Monte Carlo-based analysis approach. Once the developed linear covariance theory is validated, analysis techniques that are often prohibitory with Monte Carlo analysis are used to gain further insight into the system. These include the creation of conventional error budgets through sensitivity analysis and a new analysis approach that combines sensitivity analysis with power spectral density estimation. This new approach resolves not only the contribution of a particular error source, but also the spectrum of its contribution to the total error. In summary, the objective of this dissertation is to increase the utility of linear covariance analysis for systems with a wide variety of controllers and for whom the spectrum of the errors is critical to performance.