The Windows Group Policy PowerShell module includes a cmdlet called Set-GPRegistryValue that lets you poke values directly into the underlying registry.pol file within the
GPO, but you have to know the correct reg keys and values to do that (which you can derive from the ADMX/L files). Beyond that, commercial solutions such as our GP Automation Engine (http://www.sdmsoftware.com/products/group-policy-automation-engine/)
provide support for modifying a variety of policy areas programmatically, but it is, of course, a commercial product.