The box can be made of wood, metal or anything else. But the most simplest way of building ones box is to use plexiglass. Plexiglass under heat - from a torch, kitchen stove - will warm up and is susceptible to bending. The disadvantage of plexiglass is that its can carry electric charge - thus its unadvisable to put electronic components on the plastic - use those small plastic pegs for motherboards - glue them on the plexiglass.
The design of the box depends on your parts. If you have a small motherboard, low-profile sound card and network card, you can make the box 4"-5" tall. The placement of motherboard, power supply, and the infrared serial receiver all depends on your imagination.
In the case of my box, the minimum I could get was 6" height (the motherboard + plastic pegs + ISA Sound card). Therefore I decided on building a wide box to compensate for the height. The shape of the box is semi-pyramid.
During the design, heat and air circulation has to be taken into account. If you wish to make your system noise-less (without fans), make the box big, and drill holes on sides, and on the top so that hot air can raise and escape. You also might consider downclocking the CPU - that way you can use a heatsink instead of CPU fan. Another alternative is to drill holes one side of the box, and put a fan on other side, and have the CPU in the middle of the air-flow. Take also in consideration your power supply. The small power supplies (83W, 40W) don't exhaust too much heat and can be safely left without a fan. Unfortunately, the bigger they get the more heat they exhaust - and the heat has to be drawn out.
In my case I decided to use one fan to cool down the power supply and CPU. The fan is mounted on top of the power supply. The power supply has exhaust vents on top, from which heat escapes. The CPU is located 20cm away from the fan, under 45" angle - also not that far away from the CPU I drilled some holes to suck in fresh air. What essentially happens is that outside air is sucked in thru the holes, passes over the CPU and then combined with the air from the power supply is sucked out by a fan. For pictures: check mpeg-box pictures.