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I honestly don’t see a lot of advantages or disadvantages of one versus the other for the end user. There are a couple of things that are marginally useful that you can do with apps but not desktop programs in Windows 8. Apps can be pinned and snapped, which is nice, but certainly not vital.
The main advantage of apps is that it unifies the Windows experience and give a consistent look and feel across platforms. I do like this, but again, it falls into the nice but not vital category. If you are using a Windows 8 machine with a touchscreen, though, this is more important.
This article talks about Windows app development, you might find it of interest.