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One last question... will the Plex server be just a Plex server?
i.e. will it be in a basement, and other clients connect to it?
Or will you be connecting this to the primary TV in house that happens to be a 4k beast, and on the Plex server you'll also run Plex Media Theater?
If the former, the graphics card is irrelevant, if the latter than you'll want a decent graphics card that can be passively cooled when not in use.
I went with this one: http://www.amazon.co.uk/Gigabyte-Nvidia-Graphics-Cards-128-Bit/dp/B00UMVCYTM
It's got hardware decoders for the core video codecs you're likely to have, and the large fans are silent when it's hot, and when it's cold it's decent enough to turn the fans off entirely (saves power, keeps the room silent).
But this is not needed if the Plex server is not going to be connected to a TV. Mine is connected to a 4K TV and so I went for a 4K graphics card that can be silent.
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The aim is for it not to be connected to anything. I currently have a crappy TV that can barely manage HD let alone 4K, so at the moment everything is going via a chromecast or a miniPC I have plugged in. Will have to think about the best client to connect to the TV as don't think we want a computer in the lounge...
I would have walked straight into that trap! I will spec 4 x 3tb from different manufacturers and lob them into the qnap box.
Will then spec a fast processor small box with just an SSD to run plex off.