The schematics for the R-Pi are on the internet. Download them. Open some CAD software and make your micro Pi. Then contract to have it made.
To be honest I gave this a serious thought today and decided I just didn't have the time, and even after designing the PCB I wouldn't have the money to make the prototypes so I decided it was best left to someone else. I also tossed around the idea of designing a PCB that had a different hub/ethernet chip to facilitate more onboard USB ports. I would also beef up the power regulation to allow for some healthier overclocks. All pipe dreams though.