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The Modern UI menu shows now both Modern UI and Desktop Applications, the only difference so far is that the built-in Modern UI Apps have a simple white icon instead of a colored.

But already my first additional applications bought in the App Store have also a colored icon like any other Desktop App.

Is there a way to better differentiate, or somehow flag Modern UI or Desktop Applications?

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You just have to keep track of what applications Modern UI applications and what applications are your traditional desktop applications. You are not suppose to be able to tell the difference. – Ramhound Oct 22 '12 at 12:30
In addition to what Ramhound said, I guess the only way to keep track is to manually group tiles related to metro and non-metro apps. – Karan Oct 22 '12 at 22:11
up vote 4 down vote accepted

The easier way to differentiate them, it's the tile background. For Modern UI Apps, the color is the color chosen by the developer. For the Desktop Apps, the background is a gradient from right to left. (#333 to #666 I think...)

I use Windows 8 for over 2 months and still no other way.

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Congrats, and did you get the t-shirt? – Abid Rahman K Nov 11 '12 at 8:51
Not yet -_- But I hope! – Frederick Marcoux Nov 11 '12 at 8:51

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