The design or the realization of any project implies the involvement of a set of agents that can be individuals, teams or enterprises. These agents share resources and competencies, similar or dissimilar, and cooperate in order to reach some shared objectives by using Information Technologies. We speak then about virtual enterprise. However, exchanging data is not sufficient to support virtual enterprises, it is necessary to develop some adequate tools to guarantee a smooth functioning. Within a methodological framework for the design of inter-enterprise cooperation systems particularly in the field of virtual enterprise, we present in this paper three models of integration by data, by processes and by knowledge to support communication, coordination and collective problem-solving. We conclude this paper with a brief early evaluation of the advantages of our approach for inter-enterprise cooperation, by comparison with existing work coordination tools and architectures.