About 15 years ago I set up a wiring closet in my house. Over time I have learned some important lessons.
My house is only 1300 ft^2 with one level. It is built on a slab, so there is no basement. Fortunately the attic provides reasonably good access to the interior walls.
I ran at least one RG-6 coax, one CAT-5 (there was no such thing as CAT-6 back then) and one 4-wire telephone to a plate in every room. Most rooms have more than one plate. Some plates have two coax. Everything goes back to a central closet - really just a piece of plywood on the wall in the closet where the furnace and water heater are. I ran a dedicated 15-amp power circuit to the wiring panel with 4 pairs of outlets (16 total).
I do not subscribe to cable TV, so the coax has largely been unused. I have both television and FM antennas on the roof, and that uses a couple of the outlets to get to the back of my main hi-fi system.
The 4-wire telephone jacks also get very little use. I wish I had pulled two CAT-5 to every plate. One of them could be used for telephone systems including various PBX-like systems.
A few years after doing all of this, I added line-level audio to the wiring panel. I wish I had done that earlier. If you run line-level audio, be sure to use really good double-shielded cabling for it. I did not, and it picks up a fair bit of 60hz buzz.
I have tried some home automation stuff using X-10 devices. Some of them work and some do not. Reliability has been a big problem.
Here are my suggestions. Much of this echos comments from others.
1) You cannot have too many plates in each room. One per wall is not too many. Yes, that includes the bathrooms!
2) You cannot have too much power in each room. At least one 20-amp circuit per bedroom, preferably two, and separate from the lights in that room. At least one 20 amp circuit per wall in the family living spaces (living room, family room, multimedia room etc.) At least two or three 20 amp circuits on the kitchen counters. More 20 amp circuits in the garage and basement.
3) At least two Cat-6 per plate.
4) At least one RG-6 coax per plate. Two on some plates, especially if you think you might run a satellite or something to it.
5) At least one line-level audio pair to each plate.
6) Leave plenty of room in the conduits. Mine are jammed so full I cannot get anything more through them, and they only go about three feet from the plywood panel up to the attic.
7) Leave good stout pulling strings in every conduit.
8) Plates on the outside is a good idea. I have not needed them, but I don't have a deck or hot tub.
9) I don't really like any of the lighting controller systems that are available. X-10 is really old and lame. Insteon is not reliable. Z-Wave is hackable. Belkin WeMo depends on third-party servers.
10) Bring neutrals into every light switch box.
11) Running security wiring while the walls are open is good, even if you are not going to use it.
12) Whole-house surge protection and GFI.
13) Buy an electrical panel that is twice what you think you will need. This means both amperage capacity and number of circuits.
14) Make a provision for connecting a whole-house generator.
15) Run at least three speaker wire pairs from the front to the back of any place you might put a home theater system.
16) Run some HDMI cabling to the center of the ceiling where you might hang a projector. Also put a power circuit up there.
17) Same goes for any place you might put a VESA mount. Run HDMI, power and Ethernet to the back of any television.