I hate to tell you something you already know, so disregard if you do!
I have built countless cases out of Acrylic and used many different brands and varients. I also have experience with Polycarb in motor vehicle applications. I have NO experience fabricating with Polypropylene other than modding mounts for off road vehicles, so I won't talk about that.
You probably know this, but you need to make sure that your Acrylic is cell-cast and not extruded (sometimes called biaxially oriented). Extruded acrylic is junk and there is no reason for you to make that choice. My favorite acrylic manufacturer/brand is CHEMCAST and I highly recommend it and have used thousands of dollars of the stuff.
I don't have a particular brand favorite with Polycarb, but I can tell you the differences.
CC Acrylic is hard, which means it is harder to scratch and much nicer looking and optically clear than Polycarb. Working with thinner sheets you can score and break cleanly with the right technique. Acrylic is MUCH easier to weld than Polycarb, and that is one of several reasons it is used for fish tanks despite Polycarbs superior strength.
Polycarb is easier to machine as it is a bit softer and less prone to cracking, that being said I have machined my fair amount of CC Acrylic. Polycarb is the winner when you are talking about tapping it for threading.
Both cut fine on the tablesaw ***EDIT--USE A DEDICATED BLADE! Your metal blades will be junk after using them on plastics!!!*** , but Acrylic cuts better with slower friction tools like a dremel. Polycarb melts up fast even on slow speeds with a cutoff wheel.
Polycarb would make for an interesting case, but you probably want to use acrylic if you are going ALL plastic. Polycarb might not have the rigidity to support a motherboard at equal thicknesses without some bracing...then again maybe some flex wouldn't hurt anything and be beneficial to the durability of the system? If you wanted to combine some metal with the plastic, Polycarb would come ahead because it takes being screwed or bolted down much better without cracking.
Acrylic will be FAR better looking and last alot longer without scratches than the Polycarb though, and if you are going for clear panels that is what I would choose.
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A word of caution about painting Acrylic. The paint thinners used in spray cans can be devastating to Acrylic. I have luck with the Rustoleum brand for painting on it, but you need to apply the paint patiently by dusting and letting dry. It takes much longer to paint, but you wont have warping and chem burns showing through on the other side. I have never mixed my own paint for Acrylic so I can't help you with mixtures there. If you are working with material 5mm thick + you can paint more safely, but below that it can warp from the thinners easily.
