The very first item that matters if this is a video room, which of course it will be... WHERE DO YOU WANT THE TV?
The most common answer is: A plasma will be mounted directly above the fireplace.
This is a common and typical placement point for a TV in a decent 'home theater' environment in a modern living room.
I am also building a new home and here was my priority: DO NOT HAVE THE FIREPLACE ON THE WALL THE TV GOES ON! It took a while, but I finally found a builder who had a home that met my needs. The fireplace is on the rear wall with windows on either side and a window above it (gas fireplace). Lots of light, but still left me the back wall to properly mount my plasma and position speakers.
Okay - you may not have that option, so do you have the means to put a 42-60 inch plasma above the fireplace? Making darn sure that a mantle directs heat away from the plasma or the display will overheat and burn itself up internally.
You also need to get into some WAF issues and decide how intrusive the video setup can be in the room. For me, my wife LOVES television so not only does our video have to be prominent, it has to be easily viewable from the kitchen, dinette, and family room. We have a similar setup to what you have going in.
Now, if you can't do a plasma above the fireplace, the option is to put a display on the South (staircase) wall directly across from all those windows. This should accomodate a nice size display flanked by speakers with good center channel placement. Surrounds are still an issue, but really can be place on the walls behind you. This offers you a nice 5 channel setup. I would not over compromise on speaker placement though.
Quality speakers can be had for in-wall on on-wall mounting. Newer speakers like the Definitive Technology Mythos 2 speakers really are desiged with high WAF in mind as well as good sound. So, you can wall mount some nice looking speakers that aren't intruding on the room to much.
Do you have a basement?
I would definitely not put all the equipment directly under the plasma/tv - or I would recommend you wire for the ability to move the equipment.
Wire, wire, wire, wire. Conduit, conduit, conduit, conduit!!!
New construction is a rare event for so many aviophytes. So, use it to make sure that everything you want to do, or MAY want to do is covered. If you can't afford to buy thousands of dollars in speakers and do thousands of dollars in wiring, then DO THE WIRING! You will have money for better speakers/video later on, but this is your only solid chance to get your home wired correctly.
ALSO CONSIDER: How about audio and/or video distribution for the rest of your home if you have not done so already. If you can wire yourself especially, you can run speakers to you kitchen, dining, family rooms, deck (front and rear?), garage, and all upstairs bedrooms (don't forget the bathroom!) along with a piece of CAT5 for a control system later on. It'll take about a day or two to run those wires and you probably want a friend to help, but for a couple hundred bucks or so, all that wiring can be done by yourself easily during construction. Then the wires are there when and if you need them.
NOTE: Take photos of your home prior to drywall going up. Walk the entire house, double check wiring, and take photos of studs, wire placement, distances, etc. This will help you find old wires in a year or two if you add stuff.
Finally: Conduit... If you have a basement, getting to the main level is easy if you have an unfinished basement. But, getting from the basement to the attic may be a real nightmare. But, you should be able to run a couple of pieces of 2 to 2.5 inch conduit from the basement to the attic. This way if you add a roof antenna, DSS dish, or top floor wiring, you have access from the lowest level to the furthest level quickly and easily.
Lots to consider - have fun!