This special journal issue of Advances in Complex Systems presents a collection of papers describing current research delivered by recognized researchers actively working in various corners of the field of modeling of complex systems by cellular automata and related methods. All included papers are self-contained and present the latest developments in the areas where the authors work. Hence, all papers can be read independently, but it is strongly recommended to study the issue as a whole to get a general overview of the various methods and techniques from the field. The main aim of this special issue is to provide researchers from neighboring fields with sufficient information and vital examples of how to design models in complex systems. The whole issue is organized in such a way that common features occurring repeatedly in most models of complex systems are highlighted.