Yes entire arduino, I'm not sure if it's a good idea to have some part of it outside the box Smiley holes will be at the right place for usb connector and so on.
Is this meant to be some kind of "protective cover" for using the Arduino in an educational type environment? I mean, if its for a product based on an ATMega168/328 that you've programmed using the Arduino environment, then surely a standalone variant would be a better option cost-wise than packaging an entire Arduino board...?
I know it will cost money. I just need some factory suggestion. Thanks!
Off-hand, I don't know of any specific companies, but you are likely going to want to look into companies that manufacture "custom enclosures" and/or ones that perform "plastic injection molding"...