I was thinking of doing something like this a while ago, but I never got around to it.
First thing you should probably do is buy a cheap case, and use its parts for a template. You'll have to drill out a few rivets, but thats not a big problem. Next thing is to research what you want this case to be able to do, like a window, fan locations, drive posistion/locations, PSU location, fan/temp controller, sliding/pivoting mb, and also front face cover, since you obviously don't want some beige plastic cd drive showing.
Then ya got to design the supporting stucture to fit the features you want. Then build it(easier said then done).
I saw a mb tray that pivoted back and out, looked really cool. Also saw a lian li case that had the power supply on the bottem, and motherboard on top, very interesting, but I had doubts about its cooling.
Good thing is that your not limiting to any conventional design, bad thing is its gonna take awhile if you want it you look good. BTW take lots of pictures when you'r building because we all want to see! Good luck