PortableApps looks interesting. That said, I can't see using it with applications such as SolidWorks, CAMWorks, Xilinx FPGA tools, Altera FPGA tools, MicroSIM, various compilers, various FEA tools, Altium Designer, etc. In other words, I am talking about some major engineering applications that would probably do very poorly (if they even work) with such an environment.
As a business you would be risking all kinds of possible nightmare scenarios with compatibility, maintainability and general support issues.
The real solution has to be OS-based. Which is unlikely to happen.
As much as possible, I use PortableApps on Windows. When I migrate to a new machine, all I need to do is copy the PortableApps folder.
I don't see this as a flaw in Windows. If every application developer/packager built portable apps, there wouldn't be a problem.