Much of it is about budget.
I would say some of the most important pre-construction events that occurs is formulating the design requirements of the room.
1. Do you plan to do front projection, rear projection, plasma/lcd or something else, and at what size?
2. How big is the space you have to work in?
3. How tall are the ceilings?
4. How do you want to arrange furniture?
5. How many rows of seats?
6. What is your (realistic) budget?
There are many methods of dealing with everything, but some of the best things you can do is pull your wires early and run conduit between key locations. Think... and ask about everything. Doesn't matter that you know car audio, in many ways, but it helps. That is, in a car, you may want the lights up front that are easy to read, but in a theater, little blinking lights at the front of the room can distract from the 'theater' experience.
Front projection is awesome, but is hurt by poor lighting planning. So plan lights accordingly, or ditch the projector.
Except, a projector IS theater, and anything under 100" is just TV.
Tiered seating gets more people into the room, but requires a bit more space.
If planned properly, a projector can be pulled from the room entirely, and you can use long throw to achieve a true theater-like projection experience.
Audible noises feeding the room, including HVAC, can be real distractions, plan accordingly.
Power needs to be dedicated for certain items to improve quality and reliability.
It is impossible to pull to much wire.
Think OUTSIDE the box! If you have $10K+ in home theater gear, wouldn't it be cool to be able to disbtribute some of the audio and/or video throughout the rest of the house? If you are building, then now is the time to consider this.
I setup my home system and included about 100' of conduit in the house along with an unfinished basement. My notes on the low-voltage wiring span 11 pages. Wiring lists, distributed audio paths, equipment, etc. Everything you WANT to do, you should write down and then edit heavily to what your budget will allow.
My home has distributed HD video currently at 4 locations, with current expandability to 8 locations. It includes distributed audio to 12 locations, with expandability to 17 locations.
Yet, I don't really have a 'theater'.
All my gear is in my basement, yet none of my viewing is in the basement. Gear is remote located as necessary for easy access.
So, while focussing on the 'box' is fun, you don't want to miss your one real easy chance to step outside of the box as well for whole house audio and video...
Unless that doesn't make sense at all.
Don't forget outside!