I was wondering if anyone could elaborate any further on something that's been bugging me.

In DirectX9 the main supported back buffer formats were D3DFMT_X8R8B8G8 and D3DFMT_A8R8G8B8 (Both being BGRA in layout).

http://msdn.microsoft.com/en-us/library/windows/desktop/bb174314(v=vs.85).aspx

With the initial version of DirectX10 their was no support for BGRA and all the textbooks and online tutorials recommend DXGI_FORMAT_R8G8B8A8_UNORM (being RGBA in layout).

Now with DirectX11 BGRA is supported again and it seems as if microsoft recommends using a BGRA format as the back buffer format.

http://msdn.microsoft.com/en-us/library/windows/apps/hh465096.aspx

Are there any suggestions or are there performance implications of using one or the other?

(I assume not as obviously by specifying the format of the underlying resource the runtime will handle what bits your passing through and than infer how to utilise them based on the format.)