There is a not well documented command build into OSGeo4W Shell which sets the shell up to python3 as Luke mentions
py3_env
Basically it sets your PYTHONHOME and the correct PATH. Then you can call Python3 with python3
.
C:\>py3_env
C:\>SET PYTHONPATH=
C:\>SET PYTHONHOME=C:\OSGEO4~1\apps\Python36
C:\>PATH C:\OSGEO4~1\apps\Python36;C:\OSGEO4~1\apps\Python36\Scripts;C:\OSGEO4~1\apps\Python27\Scripts;C:\OSGEO4~1\bin;C:\Windows\system32;C:\Windows;C:\Windows\WBem
C:\>python3
Python 3.6.0 (v3.6.0:41df79263a11, Dec 23 2016, 08:06:12) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>>
Update with auslander's comment:
To use Python3 with the OSGeo4W shell that comes with QGIS 2 you have to change the file {path you installed qgis}\etc\ini\python-core.bat
:
SET PYTHONHOME=%OSGEO4W_ROOT%\apps\Python36
PATH %OSGEO4W_ROOT%\apps\Python36\Scripts;%PATH%