Expect security (at all levels, not just transport), transactions, and workflow to become widespread technologies in Web services applications. Plan to use these wherever appropriate without resorting to proprietary mechanisms which jeopardize interoperability between systems that you have not yet even dreamt of connecting.
Adding support for a protocol to a Web service even retrospectively does not affect any other supported protocols since the SOAP header processing mechanisms are extensible and modular. With Web services, adding the right mix of support for your application should be easier than ever before.
Plan to base integration projects on Web services technology unless they involve homogeneous systems. To do otherwise is a false economy since the common denominator platform that Web services provides will be supported by toolkits on most, if not all, systems that are likely to require integration effort.