One thing I'll add in here. Regular acrylic is somewhat more scratch resistant than polycarbonate. It's also noticably stiffer. Acrylic isn't so bad. Also, if you do have it all completely planned out ahead of time, some places will custom cut it for you. The place I will be purchasing my materials from will custom cut all the pieces if I want to some ungodly accuracy far better than what's needed (like 1/1000 of an inch or something I think they said). Of course, it's a bit harder because you have to have it COMPLETELY planned out in advance.
I'm still a bit unclear how you would handle mounting the motherboard. I've got a large motherboard tray I could use, but my goal for my next project would actually be to make the case as small as I possibly can.
The two possibilities I can see would be to predrill and tap holes for the brass standoffs or to use the plastic standoffs (with the nubs on the bottom cut off) and just glue them into place.