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Advances in integrated circuits and packaging technologies provided us more implementation options for mixed-signal systems. Emerging technologies are represented by system-on-chip (SoC) and system-on-package (SoP). In order to make a design decision for optimal system implementation, it is hence becoming more and more important to address the cost and performance issues for various implementation options early in a system deign phase. In this paper, we develop a modeling technique for a priori cost and performance estimations for mixed-signal system implementations. The performance model evaluates various noise isolation technologies, such as using guard rings, increasing the separation between digital and analog/RF circuitry parts, using special substrate materials (e.g., silicon-on-insulator), and partitioning the system into several chips. In cost analysis, new factors such as extra chip area and additional process steps due to mixed signal isolation, integration of intellectual property (IP) right module or "virtual components," yield and technology compatibility for merging logic, memory and analog/RF circuits on a single chip, are considered. Finally, an efficient computation algorithm, namely COMSI, was developed for cost estimation under various mixed-signal performance constraints. Case studies for SoC and SoP integration are performed using COMSI.