This is a much more common practice than I can actually stomach...
If you are doing a custom built in, then CRT is an excellent way to go as you will get the maximum image size for your dollar and one of the most incredible images. PLUS, you have the depth to handle the full size CRT. Then, you have a false front built for the CRT that makes it look like a plasma. Very cool.
The alternative - if you already have the plasma or setup done - you can get a piece of wood, the same color as your entertainment center, and mount it where the plasma will go, about 5 inches back from the front of the built in. That way, the plasma is flush with the front of the cabinetry and is not sitting back in a little pocket.
One of the coolest things I saw was a built-in that included speakers and a 50" plasma. The plasma had a door that was counter-weighted and slid up and down in front of the screen. It did not have a motor in it, but was designed so that a motor could be added later. Very trick. The cabinets that held the speakers included doors that slid back into the cabinet. Yes, you've seen those before, but these doors were faced with speaker grills, so you could keep them closed, and enjoy the music... But, when the system was off, you could slide those doors back into the built-in, and another set of doors came out the opposite direction, and were the color of the rest of the built-in. Once again - very trick.
Anyway, you do have a lot of options available to you and I would say the two most important things are:
1. Versatility! Make sure you can switch out for a larger, or different display later on. If you 'frame' the plasma, make sure you can get a new frame in 5 or 7 years if you get a 43" LCD or something like that. Make sure a slightly larger - up to say 50" display will fit the space.
2. Ventilation! Don't burn your plasma, it needs to breathe. Air flow through ventilation holes may do the job, you may need a fan added on. Especially if your source equipment is going in there as well.
