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IF you intend to build from scratch,I would suggest you research into hardware compatabiliy with as many of the cool alt-OS's written about on this site,don't worry abot M$ Windows,it runs on damn near anything but a Mac,what I'm talking about is Linux,which is probably 2nd to windows in hardware support,along with the BSD's,Next comes things like QNX and BeOS which have a more limited support base,but are definitely worth having around,especially BeOS which has some real cool multimedia tools found nowhere else,and finally,the hobby-type OS's like AtheOS-Syllable,MenuetOS,SkyOS and such.
Information can usually be found on the respective OS's sites and message boards and i would start by compiling a list of supported hardware for them all and cross-referancing it to find the common denominators so to speak.
My machines are usually optimised for BeOS,which is my favorite alternative,but sometimes I wish I would have done my homework a little more thoroughly, when I try something new and it doesn't support this or that piece of hardware that I have(of course nothing I have has actually been 'built from scratch'they are more or less cobbled together from used equipment I have aquired from various sources and upgraded with new components as needed)
This Is why I cannot stress enough the importance of"Universal Compatability"this would be one of my main reasons for building such a box,especially now when a really nice factory-made unit can be had so cheaply.