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I like some of the new metro apps and would like them to always open that way even when opened from desktop.

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This is not possible as there is no written relation between metro and desktop version of an application. They are literally two different files, and often will have different functionality.

In the case of Internet Explorer the two version use the same rendering library and hence produce the same output.

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IE does not always produce the same output, since plugins can only be used in one mode.
IE10 has an option in the desktop Internet Options settings dialog under the Programs tab to specify whether links should be open in the modern or desktop version. See How do I force all links to open in the Desktop browser? for more information.

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