Small and Medium Sized Enterprises suffers more than others from interoperability challenges. On the one hand these companies are often dependent from different larger enterprises that are dictating methods standards and technologies for collaboration. On the other hand they have to form cooperation and networks in order to fulfill customer requirements - e.g. to provide complete components as known in the car industry. The paper gives an overview about SME situation regarding Enterprise Interoperability and related research activities. In the second part a framework and integrated methodological and software service solutions will be introduced for tackling SME challenges for cooperation establishment and operations starting and ending from a business perspective. A certain part of this portfolio the extended MO(2)GO software based process assistant will be explained in more detail. At the end a research and technological outlook will be provided.