I was recently in the same boat as the OP. I don't like the thought of having to pay $100+ for a case that really wasn't exactly what I wanted, so I sketched out an idea for a cube case.
Here is the rough layout. It has separate chambers for the drives and the mobo. It also uses a semi-convection idea for cooling--cold air is brought in from the bottom, through the CPU HSF and the vid card, and out the top. My idea is to use two low-RPM 120mm fans on the mobo side and use the PSU to pull air through the hard drives. This should help to keep things as quiet as possible.
The only problems with this design are:
1. The back of the mobo is at the top of the case.
2. The top of the case is wide open. I plan on using some sort of shroud to deflect sound away from me. Not sure how this will affect airflow, though.
3. In the layout, I had planned on the mobo being attached to the outside wall of the case. I've since decided to attach it to the divider wall so that I have the option of using a window to show off the mobo.
4. Not sure if the power cables will be able to reach.
Although I've built a prototype out of corrugated, I haven't tried putting all of my parts into it yet. Luckily, one of the vendors that I work with is going to be laser-cutting the pieces. Hopefully soon, I'll be able to post pics on this.
For anyone interested,
here are the blueprints for making it yourself.
-red