I think the Jetson TK1 from NVIDIA can run mainline Linux with most of the devices working.
And to get good use out of the GPU (one of the main selling points for this platform), you'll want to use the Nvidia proprietary driver.
And yes, CUDA isn't supported by the open drivers. Other than that, I've heard Nouveau works relatively well. Though I'm not still sure if the open source graphics community has figured out a way to get stacks like Xorg or Wayland/Weston running without hacking the source on architectures where rendering and scanout are done by different DRM devices.
https://github.com/NVIDIA/tegra-nouveau-rootfs
Using a completely open stack on the TK1, from u-boot to kernel (except for the USB firmware), I can run ARM virtual machines with QEMU/KVM.