I would say ethernet all over at the very least. I prefer hard wired vs. wireless in most cases. Run CAT6 so you can use gigabit in the future (or now). Other than that, I couldn't imagine running SPDIF around the house nor could I imagine analog audio. Other than a proprietary system, ethernet is your best bet.
I was thinking this through. I decided you would, at the VERY least, want 4 ports in every room. Two on two separate brackets on different walls. Best yet would be another bracket with 2 more or even more...That would come out to 48 or more which is a rackmount switch. To do that right, get a rack and add a switch. My setup consists of switches all over the house so upgrading to gigabit would be very costly--I'd have to upgrade a lot of switches. In some cases, you would want 4 ports. The issue is that if you use one port and then have a secondary device, then you're full... having 4 on each mount would be amazing.
That's my idea on the subject. Ethernet is king at the moment. I enjoy looking at anything with an ethernet port.
I really want an ethernet thermostat for the heating/cooling system but they are over $200. I will definitely consider one of those soon if I can find one. Think of the possibilities...not only do you have a huge monitor to configure the device vs. a little screen, but it can have a lot more capabilities.
Addition: Our thermostat has times to configure but they are few and far between. They don't line up with our schedules. If I could customize it down to the minute or 5-minute period, we could save energy by not heating or cooling when we're all gone. Then you've got ethernet media players (which is what you want), ethernet cameras and security systems, ethernet for internet for devices from weather to news, sports, entertainment, everything. I'm sure new devices will be coming out soon, too.