Agent-based modelling is used in many academic disciplines so it's likely that articles about ABM will appear in many journals. The following journals (arranged by discipline) frequently feature articles that are about ABM or make use of it to study other phenomena.
The Structure and Dynamics eJournal. On their website the editors of this journal say the it "welcomes articles, book reviews, data, simulations, research material, and special issues that examine aspects of human evolution, social structure and behavior, culture, cognition, or related topics."
Computational and Mathematical Organization Theory. This journal is described as "a new perspective on organizational research by using computer simulation, logic and artificial intelligence".
Adaptive Behavior. Includes articles on adaptive behaviour in living organisms and autonomous artificial systems.
Artifical Life "investigates the scientific, engineering, philosophical, and social issues involved in our rapidly increasing technological ability to synthesize life-like behaviors from scratch in computers, machines, molecules, and other alternative media."
Ecological Modelling. According to the editors, this journal "is concerned with the use of mathematical models and systems analysis for the description of ecological processes and for the sustainable management of resources".
Journal of Economic Dynamics and Control includes "research concerning all theoretical and empirical aspects of economic dynamics and control as well as the development and use of computational method".
Journal of Economic Interaction and Coordination. This journal covers agent-based approaches to economics and other social sciences.
Journal of Mathematical Sociology. This journal focuses particularly on articles seeking "a mathematical understanding of emergent complex social structures" rather than articles that analyse individual behaviour, so agent-based modelling is likely to be particularly suitable.
Cognition and Multi-Agent Interaction. This journal "explores the intersection between cognitive sciences and social sciences."
JASSS, the Journal of Artificial Societies and Social Simulation.
Advances in Complex Systems is an inter-disciplinary journal of complex systems in fields such as biology, cognitive science, computer science, economics, engineering, physics and social sciences.
Complex Adaptive Systems Modeling covers agent- and network-based models of complex adaptive systems (CAS).
Journal of Complexity publishes research papers on mathematical and algorithmic computational complexity.
Journal of Simulation aims to provide "accessible" papers on discrete-event simulation.
Swarm Intelligence publishes mostly research articles on theoretical and practical aspects of swarm intelligence.