Why do you mention the Raspberry Pi and then mention using an atom cpu? The Raspberry Pi is in itself a computer, you wouldn't need another processor/mobo as well.
As for an Atom based netbook, because of available for purchase components, a homebuilt netbook would never be as good or as cheap as a store bought one. Manufacturers have parts made for netbooks and small computers and get them made for that purpose. A homebuilt one would probably end up being a bulky low powered Atom based Laptop.
the challenge is to make a rasperry pi into a netbook for under $300. you have to have the following:
wireless internet (any just as long as you can connect to the internet without any wires or bluetooth)
32 or 64 bit CPU (a good choice would be a intel atom)
A Screen (has to be at least 7 inch)
A GPU (if the CPU doesnt have one already)
fan(s) to keep it cool.
HARD DRIVE or at least 32gb USB flash drive
AT LEAST 1 USB PORT (not including if you used a usb flash drive as hard drive which should be inside the laptop)
battery + charger
Windows 7 or Linux as operating system.
Power ON and off button
A Case etc to fit it all in
This should be possible as long as you buy the cheapest parts.