Last generation of Intel Atoms: CedarView (D2300, D2500, D2550, D2600, D2700) and Cedar Trail (N2600, N2700, N2800) SoCs integrate a PowerVR GPU from Imagination instead of the usual Intel GPU. [...] An unsupported graphic card on Linux distributions, and which can't properly support a basic desktop environnment like Unity or Gnome 3.
Read more: https://gist.github.com/2925633. The GPU on these processors is the GMA 500, GMA 600, GMA 3600 or GMA 3650.
This may impact users wanting to run Cinnamon (though the upcoming version of Cinnamon has a "Cinnamon 2D" session, that will allow it to work), or Compiz. Before you buy a new system with an Intel Atom, check if it has one of these. (See also the comments from AlbertP on viewtopic.php?f=60&t=104919&start=20 for more background about the problems with this.)
To be very clear, this is just about these specific Intel Atom models, for which there is currently a problem on using them with Linux + hardware accelerated graphics.
Intel processors generally work very well with Linux, as Intel actively contributes to the Linux kernel and is an important sponsor and driver of Linux on multiple fronts. Just avoid these models for now when buying new hardware.
Edit: Also Intel Atom processors from the upcoming Clover Trail series again use Imagination's PowerVR GPU, and even Intel itself has now declared these processors will not work properly with Linux. Read more here viewtopic.php?f=58&t=112507. It won't be until 2013 that Intel will offer a new Atom processor series that will be fully supported on Linux.