I built my current house in 1998. Having built a house in 1994 and in just a few years been geek-frustrated with it, I did some things right the second time, and they've stood the test of time, mostly.
One, I set the entire house up as a star-configured system. No daisy-chained networks or wires. There's a central patch panel to which EVERYTHING runs. This makes debugging and tweaking far, far easier. I would absolutely do this again.
Two, I ran far more of everything than I needed at the time. That hasn't eliminated issues, but it decreased them significantly. Two Cat 5 cables, two three-conductor speaker cables, and two RG-6QS cables to every room, period. I'd do this again, but with the latest (and anticipated coming) technology.
Three, I built in an attic-to-crawlspace cable pipe. It turned out barely big enough for the four RG-6QS cables for two satellite dishes. Now with DirecTV's new combined LNBs, I'm back down to one cable and have plenty of spare room. Next time I'd put in a couple of 2" pipes instead of one 1" pipe; it would be no significant cost delta but add significant margin.
Thinking ahead, even though I have been okay for 17 years, I am still somewhat limited on expansion. I have since built on two extra rooms, and it's nearly impossible to add them to the star-configured patch panel. I am not sure I would try to do comprehensive room-to-room cable piping, because it takes a TON of piping and a very large network room to pull it off properly. Space is money when you're building a house.
What did I do WRONG?
For one, not enough photos of infrastructure before putting up the insulation and drywall. I took a ton of photos, but nearly every time I've looked at them for answering a question, I found I had somehow missed the precise shot I needed.
For another, too many places where messy infrastructure limited my options. Like cables and piping exactly where I found I wanted to add recessed lighting. I would be a lot more picky about directing the plumber and electrician where to run their stuff.
Also, I would pay more attention during design to the HVAC setup. It takes up a lot of volume, and tends to interfere with flexibility later. So I would do a better job of pre-thinking where it would go, and leave more built-in space for it.
Finally, I didn't give enough thought to house-to-street connectivity. It changes faster than my in-house systems. Every few years I have needed to have my yard dug up by the cable or telephone or electric or plumbing company. I wish there were a fairly large pipe running underneath my 150 foot driveway, through which all the necessary services could be routed and rearranged as necessary. Sort of a personal manhole thing.