32-bit

%windir%\Microsoft.NET\Framework\[version]\config\machine.config

64-bit

%windir%\Microsoft.NET\Framework64\[version]\config\machine.config 

[version] should be equal to v1.0.3705, v1.1.4322, v2.0.50727 or v4.0.30319.

v3.0 and v3.5 just contain additional assemblies to v2.0.50727 so there should be no config\machine.config. v4.5.x and v4.6.x are stored inside v4.0.30319.