Rapid technological advances in recent years have precipitated a general shift towards software distribution as a central computing paradigm. This has been accompanied by a corresponding increase in the dangers of security breaches, often causing security attributes to become an inhibiting factor for use and adoption. Despite the acknowledged importance of security, especially in the context of open and collaborative environments, there is a growing gap in the survey literature relating to systematic approaches (methodologies) for engineering secure distributed systems. In this paper, we attempt to fill the aforementioned gap by surveying and critically analyzing the state-of-the-art in security methodologies based on some form of abstract modeling (i.e. model-based methodologies) for, or applicable to, distributed systems. Our detailed reviews can be seen as a step towards increasing awareness and appreciation of a range of methodologies, allowing researchers and industry stakeholders to gain a comprehensive view of the field and make informed decisions. Following the comprehensive survey we propose a number of criteria reflecting the characteristics security methodologies should possess to be adopted in real-life industry scenarios, and evaluate each methodology accordingly. Our results highlight a number of areas for improvement, help to qualify adoption risks, and indicate future research directions.