This may not be massively innovative, but I think it is a good example of where Second Life provides a useful toolset for a real application.
Play2Train is a disaster simulation area, used by the Idaho Bioterrorism Awareness and Preparedness Program, (IBAPP) to rehearse and refine their disaster planning.
The idea is that an island (well, two islands, actually) has been set up in SL to re-create a town centre, complete with schools and other public buildings, and a virtual hospital. Disasters are created in the town, and the RL response teams have to play out their action plan within the SecondLife environment. Now simulating disasters is nothing new.... response teams or other groups have simulated disasters in classroom or model situations for quite a while. The benefit of using an environment like SL, however, is that they can play out the simulation in real-time; and have a realistic view of what is happening around them. Compare this with a simulation on a model - the participants can easily communicate with one another; they can see the whole picture of the "disaster" in the simulation. Within SL, however, participants can only "see" what they could see in RL - they cannot suddenly switch to a "helicopter view" of the whole situation (well, OK, they COULD fly, but that's cheating!). Resources will not suddenly materialise out of the blue; transportation pinch-points become apparent.
Full details of Play2train can be found at Play2Train
So, from a simple concept, SL is able to provide a rich simulation that would require a significant software effort to create from scratch. Disaster plans can be worked through and refined with a minimum of effort. Hence, my vote for Play2Train as an innovation that supports the real world.