at M.I.T. is researching into ways to better manage complexity in the engineering domain - focussed on aerospace, but with applicability for other areas. Here a list of research activities as of October 2009.
Design for safety;
Model-based system engineering;
Reusable, component-based system architectures;
Human-centered system design;
System diagnosis and fault tolerance;
System engineering of software-intensive systems;
Comprehensive Risk Management in Complex Engineered Systems
All these are the higher level research areas in software / systems engineering. CSRL are also looking at the organizational, political, and cultural aspects of system construction and operation. That, for my money, is where the "pedal hits the metal".
"Organizing for a Complex World" is a A recent good paper on this, giving a number of new insights including emphasizing flexibility and resilience in process adoption.