Possibility of rapidly forming a virtual organization (VO), triggered by a business collaboration opportunity and specially tailored to the requirements of that opportunity, is the emerging solution, specially for SMEs, and a survival mechanism in face of market turbulence (Camarinha-Matos, et al 2005). The same approach is however spreading and also becoming appealing in non-business oriented domains and contexts. Nevertheless, agility in configuration of VOs as a mission/goal-oriented collaboration networks, necessitates a-priory preparedness of organizations, which takes time and effort, and is nowadays supported within a pre-existing network called the VO breeding environment (VBE). For VBEs to properly operate and facilitate their actors, it is necessary to provide a set of automated functionalities and services supporting the necessary activities and processes that can ultimately assist with the agile/fluid creation of VOs within the VBE, namely the existence of a VBE management system (VMS). This chapter addresses a number of services/functionalities that are fundamental for the VMS. Among others, they include services for supporting the management of the VBE ontology and specially the management of the organizations' competencies, assessment and management of trust among the organizations, the structuring of VBE memberships, the management of VBE's Bag of assets, and the processes related to decision making in VBE environment.