Multi-agent systems (MAS) have been of interest to many researchers during the last decades. This thesis focuses on multi-robot systems (MRS) and programmable matter as two types of MAS. Regarding MRS, the focus is on the 'mergeable nervous system' (MNS) concept which allows the robots to connect to one another and establish a communication network through self-organization and then use the network to temporarily report sensing events and cede authority to a single robot in the system. Here, in a collective perception scenario, we experimentally evaluate the performance of an MNS-enabled approach and compare it with that of several decentralized benchmark approaches. We show that an MNS-enabled approach is high-performing, fault-tolerant, and scalable, so it is an appropriate approach for MRS. As a goal of the thesis, using an MNS-enabled approach, we present for the first time a comprehensive comparison of control architectures in multi-robot systems, which includes a comparison of accuracy, efficiency, speed, energy consumption, scalability, and fault tolerance. Our comparisons provide designers of multi-robot systems with a better understanding for selecting the best-performing control depending on the system's objectives. Additionally, as a separate goal, we design a high-level leader based programmable matter, which can perform some basic primitive operations in a grid environment, and construct it using lower-level organisms. We design and implement deterministic algorithms for "curl" operation of this high-level matter, an instance of shape formation problem. We prove the correctness of the presented algorithms, analytically determine their complexity, and experimentally evaluate their performance.