Based on the room layout, it does seem that your gear is going to end up in a piece of furniture, as Tim said. That doesn't necessarily have to be a floor standing rack, though. I did a custom home in Breckenridge where the A/V components were housed in an enclosed shaker style coffee table with sliding doors facing the sofa. They too had only a few components and the dimensions of most coffee tables are deep enough for one component and wide enough for two. In your case, the amp on one side and the PS3 & Rogers box stacked on the other. I wouldn't worry about over heating with this configuration, I instructed my clients to slide the door open to the amp when they were watching a movie or if they kids were playing video games. Furthermore, this configuration created a very convenient place to stuff the game controllers when they weren't being used. Now, I did have to have the sparkies set me up with a 110 plate in the ground where the table went, and monitor cables had to be run through the floor joists to the tv wall. Furthermore, the coffee table was pretty much relegated to that spot in the room, so it has its drawbacks. I don't know what kind of sub-floor you're working with either, this may not even be an option. Here's an example of that table.
Also, the Harmony's are great devices and easy for the family to use. Like most advanced universals, they are macro driven which has its drawbacks. If the macro sequence is disrupted in any way - RF interference, break in line-of-sight (for IR models) or a component that was manually turned off - the macro does its job but doesn't effectively perform the operation. With these remotes, I spend A LOT of time training the entire family how to use it comfortably. IF used properly the Harmony remotes can be a godsend for family members that aren't comfortable with electronics. What separates Harmony is their user-friendly PC driven user interface. You plug the remote into the PC w/ a USB cable, install and run the software, tell the wizard exactly how you have your system wired and which models you're using and it does the rest. Furthermore, you remote's configuration is backed up on your PC, so even if the remote was "wiped," you could simply re-flash it.
For your AVR, the sony may work fine. Depending on the model and age, it may or may not switch HDMI. If so, 1080p is at your doorstep and you should buy the biggest damn tv that fits aesthetically to maximize all those pixels. If not, component video (3xRG6) from the receiver to the tv will support 480p/720p/1080i analog signals. The difference in video quality from a 720p component feed and a 720p digital HDMI feed is negligible. The difference, however, between a 720p and a 1080p feed on a large tv is striking. To take full advantage of the blu ray player in your PS3, you're going to want to send HDMI to the tv. You don't necessarily need to upgrade your amp to do this either. You can run a dedicated HDMI monitor out from the PS3 to the TV and pipe the audio via DigOptical into your amp (which I'll guarantee your sony has). This, however, creates a second switching process. The TV input must be changed along with the AVR input when you want to run your PS3. This problem is a minor inconvenience and can be solved by a remote (with macros, of course!) and it will save you some money, which is a good thing because that HDMI cable is not going to be cheap! As far as receivers go, I stand by Denon and Yamaha until the day I die. They both use extremely high quality construction and internals and consistently offer the most features for the price, period. A $300 - $400 Denon or Yamaha receiver will sound amazing, have most (if not all) the features you'll need and will last a lifetime. Audio equipment doesn't antiquate as quickly as other consumer electronics and with the industry settling on HDMI as a standard, a solid AVR could realistically last you 20+ years if you buy the right unit.
As far as the TV goes, if you're planning to watch blue ray, get as much tv as you can afford, and is aesthetic. I am not a huge supporter of the "eye fatigue" argument in home theater. Right now, I'm sitting 18" away from a 19" monitor and do so countless hours a week! So, if your sofa was 14' away, you could support a 15' TV! I'm just kidding but I wanted to illustrate a point. In the room you've so clearly diagrammed, your TV size is going to be limited only by aesthetics. If it were my job, I'd find the biggest tv that would allow me to mount flush with the tops of the two windows and create a some what even 3-6" frame of wall space between the sides of the tv and the window and the bottom of the tv and the fireplace. Don't worry about height for optimal viewing. Any $150 plasma mount will allow you to tilt down about 15 degrees or more which is usually more than enough to optimize viewing. Also, I don't know what direction the fireplace wall faces but coverings are going to be crucial for those windows.
As far as furniture placement goes, in a case like yours - it is what it is. It looks like your sofa is going to have be in the middle of the room, with space behind it for the stairs and computer desk. You can have individual chairs on either wall adjacent the fireplace but viewing won't be optimal. You could place a chair on only one of the side walls and utilize a cantilever wall bracket for the plasma that will allow you to angle it horizontally and down toward one corner of the room. The tv can be pushed back flat against the wall while it's not being used. These brackets, however, aren't cheap. Furniture placement is dependent on the number of people you envision watching the tv at the same time and your options are limited. A sofa for 3 or 4 viewers in a pretty optimal position and either one or two flanking chairs with slightly less optimal viewing angles.
I hope this helped!
Josch