What is the better way to convert program in portable format?

I think first it would be the cost of the Thinapp ($$$$)

The two methods are VERY different, to the point that comparing them is like trying to compare making a hand-made item vs. a mass-produced item - the end product is essentially the same, but the process to get there is very different.

Our method uses a lot of manual (as in done by the developer) detection to determine what portability is needed. If something is missed or doesn't work properly, it is solely the developers issue. We also don't interfere in any way with what the program does in its normal lifecycle, the PortableApps Launcher just sets up before execution and cleans up after execution for things like registry and filesystem changes. We also don't do much in regard to external dependencies except for detecting Java (and in an upcoming version detecting .NET framework versions) and warning if it isn't present on the computer you are using it on.

The way ThinApp and similar virtualization programs do it is to automatically intercept registry and filesystem changes and redirect them within their own package - there is very little developer interaction, but the offset for that is that when things go wrong there also isn't much you can do to fix it. They also try to identify and include external dependencies like Java and .NET within the package (and they usually fail).