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System-on-package (SOP) is a viable alternative to system-on-chip (SOC) for meeting the rigorous requirements of today's mixed-signal system integration. Thermal integrity is arguably the most crucial issue in three-dimensional (3-D) SOP due to the compact nature of the 3-D integration. In addition, the power supply noise issue becomes more serious as the supply voltage continues to decrease while the number of active devices consuming power increases. We propose a 3-D module and decap (decoupling capacitance) placement algorithm that evenly distributes the thermal profile and reduces the power supply noise. In addition, we allocate white spaces around the modules that require decaps to suppress the power supply noise while minimizing the area overhead. In our experimentation, we achieve improvements in both maximum temperature and decap amount with only small increase in area, wirelength, and runtime.