Skip the Shuttle system and build something else. Shuttle has not ever, does not now, and likely will never, build a quiet system. Not by any stretch of the imagination.

If you must have only a single system that both holds and plays the media and it must be located in the room with the TV, then splurge and get a big amp-sized case that uses no fans, like the HFX: http://www.hifiatx.com/hfx.php?lang=EN

If you can have a server located somewhere else (recommended) then build a smaller and less powerful machine for playback. Also using a fanless case, but this one can be low profile - put a notebook HD in it.

When I move in February I'm locating the media-playing and serving PC in the basement approximately under where the TV will go. The only thing coming into the living room will be audio/video cabling and a thin wire for the USB IR receiver. But if I was rebuilding from scratch, I don't think I'd start with anything other than an HFX case.