To go back to the components side a bit, you might want to look at unifying what company you buy everything from. Many are offering nice links between their equipment over HDMI to make things easier to control. Sony for example has a feature in most of their products now called "Bravia Link". This allows all the devices to seamlessly integrate into the interface on the TV. You can then just use one remote to control most of the functions you would need. It looks like Samsung calls theirs "Anynet".

On the media/PC side, you may be able to skip the box under the TV completely, as some offer DLNA compatible network streaming either built in, or via a box that attaches to the back of the TV.

Features like this are why I will probably look at replacing my system at some point in the future all in one go.