There are a number of vendors who offer Arduino-compatible bare PCBs in various configurations (and degrees of compatibility.) You have the "Really Bare Bones Board"
from Modern Devices (which is pretty much the bare minimum you need to add to the chip to have a working system, but is not "shield shaped", through the Freeduino Bare boards
offered by NKC Electronics (and there are flat-out clone vendors/pirates that sell bare boards via eBay.)
There are also assorted versions with "extra" stuff on them that may be interesting. Since the Arduino is open-source, you can also download the PCB design files, modify them as may be useful for your particular application (or not) and have your favorite PCB vendors make as many as you'd like...