Need help wiring (TV-Cable Box-DVD-Surround Receiver)

I need some help understanding how to wire up my tv and sound.

I'm refinishing my family room and am planning for a 5.1 surround sound system, and am putting all of the cable box and receiver components in another room.

The components I have going on are:
58" TV
Blu-Ray 3D DVD player
Surround Sound Receiver (Still deciding which)
Surround Sound Speakers (5.1 setup)
IR Repeater

Questions:
1.) What type of wire should I be using between these components? HDMI's all around? Any Digital Optical or S-Video needed between the receiver or anything, or will HDMI pass all the info?

2.) If I am passing the cable wire to the cable box first, and then to the receiver, and then everything else through the receiver does make it more difficult to control the other components since they are passing through the receiver? Or does the receiver just need to be on, and then everything else will function properly?

I tried to use this wiring diagram creator online and this is what it showed me, is this the best way? Click the link and scroll down and you'll see the setup it recommends.
Wiring with HDMI's

Here is another diagram that uses S-Video and Digital Optical, but am unsure if the DVD player are passing through the receiver or what not:
Wiring without HDMI's


I'm a newbie at this stuff, I appreciate the help

Thanks for the break down.
So it looks like 1 HDMI and a possible Cat5 cable.
I'm passing a plastic tube with an open style wall plate so I can pass the cat 5 cable once the walls are closed up.

So the IR systems run on cat 5 typically? I saw one cheaper one was on a 3.5mm jack style head phone cord, guess the cat 5 couldn't hurt but my receiver and tv are both wifi.