Yes, you can reuse your HTML markup in a Windows Store app based on HTML/WinJS. The exception is that all the resources must be local to the app package. For example, you cannot reference a <script> tag to download a script from a http location. The
following link gives a general comparison guidance:
http://msdn.microsoft.com/en-us/library/windows/apps/hh465373(v=VS.85).aspx