If you have basement access, then you might consider just dropping a few pieces of 3/4" conduit to several locations now. It will make access that much easier should you need it later on. Blue 3/4" flex conduit is available from Home Depot for about 3 bucks for 10 feet. I picked up 100 feet at
www.smarthome.com and put it to use.
I would stronly recommend lighting control and looking at low voltage (IR) control of lighting which may mean that you will want an IR emitter at the light - run CAT-5 to each light switch in the room. Likewise, if there is a gas fireplace, you may be able to add control of that to your remote - or upgrade your remote to allow it.
While the drywall is important to consider, I have to say that the built in really is the true drywall and it is much more. It is going to force your position on every speaker, the size of the TV, the access to your equipment, and the ability to wire in the future. This is the single most important thing to think out and ask about before it is built.
How will your equipment receive ventilation? Will it just be open air, sitting on shelves, or will it have cabinet doors on it?
How will you access the equipment? Do you know how much fun it is to try to wire up a 5.1 (or more) system by holding a 40 pound receiver in one hand and putting the speaker wires in place with the other... then trying to get it all back into cubby hole on the shelf? You may want to consider a slide out equipment rack from a company like Middle Atlantic (
www.middleatlantic.com) so that you can properly wire up your system and change compnents as necessary.
How will wiring be handled within the built-in? The best way I have seen is having shelves that have a 2-3 inch gap behind them so that wires can be put down or up as necessary. Much better than holes that get filled up with a lot of wires.
How are you going to tie all the equipment into your home distributed audio system? Will you buy another CD changer, tuner, etc. for the house audio? Maybe consider runs between the two locations now.
IMHO doing a custom room and putting all of your equipment right up at the front of the room is distracting. You used to have to put all your equipment at the front of the room, like your receiver, DVD player, VCR, etc. Now you can put it in the basement or the equipment closet and just put the DVD & VCR in a cabinet next to your couch if you want. But, with the built in, it may just be better to put it all where everyone else puts it.
Anyway, conduit most definitely is your friend and takes about 5 minutes per location to install and makes adding wires later much, much easier.