Q:

How do I get Castle Windsor to ignore certain routes/controllers? 

I'm using a third party API and Castle Windsor's default controller factory.  Unfortunately this third party API has some controllers they are using that are being instantiated by something other than Castle Windsor.  So basically in my method I need to say, ignore these controllers/routes, how would I do this? 
Here's my factory:
public class WindsorControllerFactory : DefaultControllerFactory
{
    private readonly IKernel _kernel;

    public WindsorControllerFactory(IKernel kernel)
    {
        _kernel = kernel;
    }

    public override void ReleaseController(IController controller)
    {
        _kernel. ReleaseComponent(controller);
    }

    protected override IController GetControllerInstance(RequestContext requestContext, Type controllerType)
    {
        if (controllerType == null)
            throw new HttpException(404, string. Format("The controller for path '{0}' could not be found.",  requestContext. HttpContext. Request. Path));

        return (IController)_kernel. Resolve(controllerType);
    }
}

A:

I guess you are registering the components by convention.  In this case just change the registration so that controllers that match the third-party API are not registered by using an Unless clause
container. Register(
    Classes
    .FromAssemblyInThisApplication()
    .InSameNamespaceAs<Controller>()
    .Unless(type => type. Name == "NotThisController" || type. Namespace. Contains("NotHere"))
    .WithServiceAllInterfaces());

This is where careful organisation of your namespaces, classes and structure can pay off :)
Edited to add: stuartd's comment made me realize that I didn't explicitly explained the next step.  In your factory you then check for the existence of the type registration and route to the correct resolution mechanism:
protected override IController GetControllerInstance(RequestContext requestContext, Type controllerType)
{
    if (controllerType == null)
        throw new HttpException(404, string. Format("The controller for path '{0}' could not be found.",  requestContext. HttpContext. Request. Path));

    if (!_ kernel. HasComponent(controllerType))
    {
         // return the component with your custom third party resolution
    }

    return (IController)_kernel. Resolve(controllerType);
}

