Pick one location for an equipment head-end where everything will go. That is where everything should be wired to. Also consider EVERYWHERE you want, or may want wiring.
I have the following rooms wired, or fully outfitted in my home for not just speakers, but for control, phone, lan, cable, and sometimes conduit:
Family room (everything plus)
Kitchen (speakers, control, phone, cable, future access)
Rear Deck (speakers, control)
Dining Room (speakers, control)
Living Room (speakers, control)
Study (speakers, control, conduit, LAN, phone)
Garage (speakers, control)
Front Porch (speakers, control)
Master Bed (speakers, control, conduit, phone, lan, cable, lots of extra access)
Master Bath (speakers, control, conduit (for possible future behind mirror TV)
3 more medrooms (speakers, control, lan, phone, cable)
Guest bath & laundry (speakers, control)
It is all wired to the basement under the stairwell where all the equipment resides, including phone, lan, and cable distribution. Since the area is under the stairs it doesn't cut into the rest of my home or intrude at all. The basement is unfinished so there are endless possibilities down there.
There is a pre-wire your home guide on the main AudioHolics site that is a good read, as well as the post in the forums that discusses it.
EDIT: Bottom line is that during construction is the time to prewire, prewire, prewire. Conduit is a big plus, especially from the head end to the attic or rooms that really may need to be upgraded. Once the drywall is up, it is the wrong time to decide that you need an antenna on your roof (dish, DirecTV, off-air) if you haven't prewired for it, or put conduit in for proper access. Plus, you can usually roll the prewire labor into the mortgage.