I definitely see a future for portable applications, but I have a few concerns about the technology that I think will hold it back. First, there is the issue of security. I agree with Alex.Norton that companies may be hesitant to make it easy for you to put their product on portable media when there's the potential for a program similar to CloneCD, let's call it CloneUSB, to come along and allow for ease in piracy. Second, there is the issue of consumer appeal, something that I mention here for completeness. While PortableApps is open source and therefore 'tinker-around-able', something I enjoy doing, some of the other options to this point (I'm pointing the finger at U3 software) have been, in my experience, intrusive.
So what is the future for PortableApps? I see it picking up many more freeware plugins, continuing the trend evidenced on its website. As for the large, closed-source CAD packages, I predict that they will eventually become PortableApps compatible, but may require a computer with web-access so the program could authenticate itself against some password or certificate database. While it would still be possible to pirate the software, since the barriers to do so are the same (registering the product during the installation), it would be just as difficult as now, and since the companies do make the product now, then it's an acceptable level of risk to piracy that they are willing to endure.