And that reason is ISA. In my organization, we have lots of first generation Pentium's running Win 95. They are slow, a pain to administer, detached from the rest of the network out of necessity.
There's nothing we'd like more than to get rid of the dinosaurs, but we have to keep them because they host various ISA boards that are essential to our operations. For instance, we use one system to plot points on the stage of a microscope. It has an ISA interface card. Its not easy to find new hardware that supports ISA, so when one of these things goes (and they will go) we are kind of stuck.
It would be great to buy a beefy Athlon 64 and let it run all of these things as virtual machines, but due to ISA its out of the question.
The other thing we use DOS systems for are real time tasks. Can't run a real time system on a virtual machine, of course. I know there are other RTOS out there, but we have a very significant investment in DOS applications (I didn't believe it before I got here).