Connect your own PCB to a Raspberry Pi with Raspberry Pi GPIO Header - Extra tall 2x13 Female Header. The female header part has extra spaces to make it 13.6mm tall: when placed on your Pi, a PCB will clear the Ethernet and USB jacks. This header has 3mm of pins, compared with the stacking version which is the same base height but has 9.7mm height instead. With 3mm you don't have to cut the really long pins, so it’s ideal for basic Pi plate design.
Adafruit Website: http://www.adafruit.com/products/1658