Enterprises which are distributed in space and/or which are composed as a temporary joint venture of legally different units recently often called virtual (extended) enterprises. Planning, design and operation (management) goals and requirements of such firms are generally different from those of single, centralized enterprises. The basic feature of an extended (virtual) enterprise is that the co-operating units of it keep their independence during the life-cycle of the co-operation-what is well regulated by the rules of the given conglomerate. It has to be accepted-on the other hand-that several basic functionalities and goals are the same for all types of distributed, large, complex organizations, which are the targets of our recent study.The evolution of web-based manufacturing design/planning and operation system philosophies can be followed through the works presented in this paper. We intend to give software solutions for design, planning and operation (management) of complex, networked organizations represented as nodes of networks. In the first part of the paper, solutions are given to manage complex logistics flows of distributed SMEs, giving more sophisticated solutions than the commonly used supply-chain management (SCM) packages available in the market. The second problem we solve is a complex, web-based solution to manage large, expensive, multi-site, multi-company projects using any type of Enterprise Resource Planning (ERP) and flow management solutions. Our goal is to integrate as many available solutions as possible and to make only the appropriate frameworks including decision-support systems where necessary. The first part of the work means the establishment and application of a web server at each node of the co-operating network, while the second approach uses only one, joint web server and each node communicates with it through the network. These architectures are easy to be integrated if needed, i.e. logistic flows and project management can be solved together. #