HttpControllerActivator.cs

//This is for your web api controllers.
public class HttpControllerActivator : IHttpControllerActivator
{
	private readonly IContainer _container;

	public HttpControllerActivator(IContainer container)
	{
		_container = container;
	}

	public IHttpController Create(
		HttpRequestMessage request,
		HttpControllerDescriptor controllerDescriptor,
		Type controllerType)
	{
		var nestedContainer = _container.GetNestedContainer();
		nestedContainer.Inject(typeof(HttpRequestMessage), request);
		nestedContainer.Inject(RequestKeys.BusinessKey, request.BusinessId());

		request.RegisterForDispose(nestedContainer);
		return (IHttpController)nestedContainer.GetInstance(controllerType);
	}
}

IoC.cs

public static class IoC
{
	public static IContainer Initialize()
	{
	  //... do the IOC type things in here.
  }
}

MvcControllerFactory.cs

//This is for asp.net mvc controllers. Based on Stig Christensen's example at
// https://groups.google.com/forum/#!topic/structuremap-users/ELY2g0dwUIo

public class MvcControllerFactory : DefaultControllerFactory
{
	private const string NestedContainerKey = "NestedContainer";
	private readonly IContainer _container;

	public MvcControllerFactory(IContainer container)
	{
		_container = container;
	}

	public static void DisposeNestedContainer()
	{
		var nestedContainer = HttpContext.Current.Items[NestedContainerKey] as IContainer;

		if (nestedContainer != null)
		{
			nestedContainer.Dispose();
		}
	}

	private IContainer CreateOrGetNestedContainer()
	{
		var nestedContainer = HttpContext.Current.Items[NestedContainerKey] as IContainer;

		if (nestedContainer == null)
		{
			nestedContainer = _container.GetNestedContainer();

			HttpContext.Current.Items[NestedContainerKey] = nestedContainer;
		}

		return nestedContainer;
	}

	protected override IController GetControllerInstance(RequestContext requestContext, Type controllerType)
	{
		return CreateOrGetNestedContainer().GetInstance(controllerType) as Controller;
	}
}

StructuremapMvc.cs

[assembly: PreApplicationStartMethod(typeof(StructuremapMvc), "Start")]

namespace TheThing.Web.App_Start
{
	public static class StructuremapMvc
	{
		public static void Start()
		{
			var container = IoC.Initialize();

			ControllerBuilder.Current.SetControllerFactory(new MvcControllerFactory(container));
			GlobalConfiguration.Configuration.Services.Replace(typeof(IHttpControllerActivator), new HttpControllerActivator(container));
		}
	}
}

Your global.asax.cs

//in your global asax, you'll want to ensure you're disposing of your nested container at the end of the request. 
//Note, this is for mvc controllers only. The web api http controller resolver registers itself for disposal.
public class MvcApplication : HttpApplication
{
	protected void Application_EndRequest(object sender, EventArgs e)
	{
		MvcControllerFactory.DisposeNestedContainer();
	}
}

I don't have a use case that requires DependencyResolver and the MvcControllerFactory. Are you using that for resolving attribute dependencies?

@khalidabuhakmeh Want to spin up a small repo with an example filter? Or, I could.

I was using a similar approach.

My Sm web activator used to look like:

[assembly: PreApplicationStartMethod(typeof(StructuremapMvc), "Start")]

namespace TheThing.Web.App_Start
{
    public static class StructuremapMvc
    {
        public static void Start()
        {
            var container = IoC.Initialize();

            DependencyResolver.SetResolver(new StructureMapDependencyResolver(container));
            GlobalConfiguration.Configuration.Services.Replace(typeof(IHttpControllerActivator), new HttpControllerActivator(container));
        }
    }
}

However, the details behind the SM resolver I was using are a bit more involved. I believe it was the StructureMap.MVC4 nuget package (code-only package so worth looking at)

I suspect it'd be fine to set both the dependency resolver and a controller activator. However, we'd want to see if we can notice any weird behavior where it's creating a separate child container.