The main objective of this dissertation is to explore and develop computer-aided-design (CAD) methodologies and optimization techniques for reliability, timing performance, and power consumption of through-silicon-via(TSV)-based and monolithic 3D IC designs. The 3D IC technology is a promising answer to the device scaling and interconnect problems that industry faces today. Yet, since multiple dies are stacked vertically in 3D ICs, new problems arise such as thermal, power delivery, and so on. New physical design methodologies and optimization techniques should be developed to address the problems and exploit the design freedom in 3D ICs. Towards the objective, this dissertation includes four research projects. The first project is on the ...