Many core modern multiprocessor systems-on-chip offers tremendous power and performance optimization opportunities by tuning thousands of potential voltage, frequency and core configurations. Applications running on these architectures are becoming increasingly complex. As the basic building blocks, which make up the application, change during runtime, different configurations may become optimal with respect to power, performance or other metrics. Identifying the optimal configuration at runtime is a daunting task due to a large number of workloads and configurations. Therefore, there is a strong need to evaluate the metrics of interest as a function of the supported configurations. This thesis focuses on two different types of modern multiprocessor systems-on-chip (SoC): Mobile heterogeneous systems and tile based Intel Xeon Phi architecture. For mobile heterogeneous systems, this thesis presents a novel methodology that can accurately instrument different types of applications with specific performance monitoring calls. These calls provide a rich set of performance statistics at a basic block level while the application runs on the target platform. The target architecture used for this work (Odroid XU3) is capable of running at 4940 different frequency and core combinations. With the help of instrumented application vast amount of characterization data is collected that provides details about performance, power and CPU state at every instrumented basic block across 19 different types of applications. The vast amount of data collected has enabled two runtime schemes. The first work provides a methodology to find optimal configurations in heterogeneous architecture using classifiers and demonstrates an average increase of 93%, 81% and 6% in performance per watt compared to the interactive, ondemand and powersave governors, respectively. The second work using same data shows a novel imitation learning framework for dynamically controlling the type, number, and the frequencies of active cores to achieve an average of 109% PPW improvement compared to the default governors. This work also presents how to accurately profile tile based Intel Xeon Phi architecture while training different types of neural networks using open image dataset on deep learning framework. The data collected allows deep exploratory analysis. It also showcases how different hardware parameters affect performance of Xeon Phi.