The ever-active Patterns and Practices group have released Guidelines for Application Integration focussing on EAI Architectures.   It provides useful coverage of all of many of the issues involved in integrating applications.

The guidelines covers the levels of application integration, such as business process, data and communications-level integration.  It defines the capabilities required at each of these levels.  It also covers security and operational considerations before finally showing how to map Microsoft Technologies to application integration capabilities.

The guide is useful because it deals with concepts from an abstract perspective rather than a technology-centric approach.  All of this is likely to be useful in a service-oriented (it's just not PC to say SOA anymore) world.  The architectural concepts and business issues identified are independent of the technical implementations such as Indigo.