If I haven't decided on my whole-house audio or video system, can I reasonably design the structured wiring? By that I mean, should I simply run Cat5 or 6 to every room, along with a return Cat5 line and decide later on whether to have a Niles, Russound setup, or something like Zon?
Run 2 Cat5/e/6 and 2 RG6 cables to every wall of every room. Also, run speaker wires where you want them (don't forget the pool/deck/lanai area) and don't forget to run power and cables to wall mounted TV locations. Also, run conduits to the wall mounted TVs for A/V cables.
You've specified systems that have centralized amps, and systems that have keypad-based amps. If you want to accommodate both, you'll have to run speaker wires to each speaker from both the wiring closet and the keypad location in each room. (Or run a single pair of speaker wires from the wiring closet to the keypad location, loop it a few times, then continue on to the speakers)
One way is to run 4-wire 14ga to the keypad locations and then run 2-wire
14ga to each left/right speaker location. It's usually easier to run a
4-wire home run than two 2 pairs. Inside the box you splice the connection with something like small eurostyle terminal blocks. Otherwise you end up running the 4-wire all the way through to one speaker location and then over to the other. Not always as easy as running each leg independently. But if the walls are already open it's just a matter of preference and possibly some (small?) difference in costs for the wire.
By running the wire throught the wall plate junction box you can accomodate either style of system; central or keypad amps. For central amps you just splice through, for keypad amps you end up ignoring the home-run lines. As in, if at some point you want to switch from A-Bus to Russound CAV66 (or zon or whatever) you won't have to pull any new wire. Bear in mind there are some special situations you may want to plan for ahead of time. Like wanting to use in-room devices with the in-wall speakers. Some systems handle in-room inputs locally while others require home-run or other things for it. Most of the time it's a lot less hassle to use central equipment than to try integrating in-room stuff.
Your point is well taken. Since the distance from the room to the central wiring harness doesn't really degrade the signal, it's probably easier to do maintenance in one place. That means using the Cat5 systems that run the controller back to the central area, and running the speaker wire all the way from the central service point. I'm still new to this stuff, and just figuring out the needs, let alone the means, is hard enough!