Windows

According to AnandTech:

Windows 7 by default starts up at 800 x 600 on the Retina MBP, Windows 8 defaults to 1024 x 768. This behavior isn't specific to this system, the GeForce GT 650M doesn't have native driver support in either OS at this point and these are the defaults for the standard VGA driver in both cases.

Windows 7 won't expose any resolutions higher than 1600 x 1200 without an actual NVIDIA driver, while Windows 8 will let you select the full 2880 x 1800 panel resolution.

This is a report about Windows via bootcamp. I don't know how this differs from Windows being used in a virtual machine. It would probably also depend on the options that the VM software offers.

Linux

When using the NVIDIA drivers on Linux (and on Windows too) you can select the full native panel resolution (2880x1800). You can also select any of a number of scaled resolutions which don't look as sharp. In general, running at native resolution is actually less of a problem for Linux than it is in Windows and OS X because of the way it's designed. There are no blurry fonts on 3rd party apps like on OS X and it is easier to set your DPI so that apps are scaled properly than on Windows (it is set automatically in Linux).