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".
In theory this is a great idea - it would ideally work with components from any brand. In practice it's not that great because you'll have to stick with a single brand. No single brand offers high quality gear in every product segment.
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".
A decent universal remote such as one from Universal Remotes or a Harmony will be able to deal with the multiple devices. It may be easier than using the included remote from any one of the devices, even if they interlink.
I don't think there's huge value in pairing audio processing gear with the same brand video display gear. The video display for the most part can be treated as a dumb display device that needs not much more than an ON and OFF control. This is especially true is using an external video processor. Many receivers today have video processing in addition to audio so you only need a single device to control switching and all processing, plus of course amplification.
As Taym suggested, the Onkyo stuff is pretty good and gets decent reviews. Likewise so too is their Integra brand (including the DHC-9.9 AV Pre-Pro I'm looking at right now). They have Receiver (with power amplification) and Pre-Amp (without power amplification) versions of their components.
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.
The issue here is going to be format support and updates. There's a lot to do here, from container formats to audio and video codecs. You'll find most products in all classes are fairly short in this area. It's a rare component that caters to all formats. Support in a TV is likely to be on the very short side when compared to something like an Extender or Media PC which can see quicker updates duue to its position in the ecosystem and lower install base (much more risky rolling out updates to 1 million grandmas' Sony TVs than a few thousand enthusiasts).
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