The second I-ESA international conference, supported by the INTEROP NoE (Interoperability Research for Networked Enterprises Applications and Software Network of Excellence, http://www.interop-noe.org) and the ATHENA IP (Advanced Technologies for interoperability of Heterogeneous Enterprise Networks and their Applications, http://www.athena-ip.org) and sponsored by IFAC and IFIP, offered a workshops program comprising three workshops and a Doctorial Symposium. The objective of the workshops that held on March 21st, 2006, was to strengthen some key topics related to interoperability of enterprise applications and software. The workshops organisation left time slots for brainstorming among the attendees in order to come out, at the end, with possible new research directions. The Doctorial Symposium provides an open forum for students involved in the preparation of their PhD to discuss their research issues and ideas with senior researchers. These proceedings include papers from the three workshops (EI2N'2006, WSI'2006 and IS-TSPQ'2006) together with peer reviewed contributions to the Doctoral Symposium.