This post may help (I have not tried it but you might be able to adapt the approach for the file manager):

http://world.episerver.com/Blogs/Anders-Hattestad/Dates/2011/6/How-to-change-context-menu-in-the-edit-mode-tree-view/ 

Hi David,

Thanks, thats actually the approach I've used. The reflection isn't necessary as ActionWindow inherits pagebase and thus exposes a ContextMenu property - problem is its always null in the PageSetup event handler. I'm guessing I'm trying in the wrong time in the lifecycle or the ContextMenu is possibly set on a PlugIn contained within the ActionWindow object?

You can try hooking in on PreRender using an init module. (untested) Example below:

[InitializableModule]
[ModuleDependency((typeof(EPiServer.Web.InitializationModule)))]
public class AddContextMenu : IInitializableHttpModule
{
    private static bool _loaded = false;

    public void InitializeHttpEvents(System.Web.HttpApplication application)
    {
        application.PreRequestHandlerExecute += context_PreRequestHandlerExecute;
    }

    private void context_PreRequestHandlerExecute(object sender, EventArgs e)
    {
        //Get the Request handler from the Context
        HttpContext context = ((HttpApplication)sender).Context;

        //Check if the request handler is a PageBase object
        if (context.Handler is EPiServer.PageBase)
        {
            PageBase pageBase = (PageBase)context.Handler;
            pageBase.PreRender += page_PreRender;
        }
    }

    private void page_PreRender(object sender, EventArgs e)
    {
        if (sender is ActionWindow)
        {
            // Code to hook into menu here

        }
    }

    public void Initialize(EPiServer.Framework.Initialization.InitializationEngine context)
    {
        //throw new NotImplementedException();
    }

    public void Preload(string[] parameters)
    {
        throw new NotImplementedException();
    }

    public void Uninitialize(EPiServer.Framework.Initialization.InitializationEngine context)
    {
        //throw new NotImplementedException();
    }
}

Thanks again David, unfortunately no luck! I definitely think I'm going about this the wrong way and assume the context menu when right-clicking on a file is actually being set somewhere in EPiServer.UI.Hosting.VirtualPathFileManager, just can't see where. I think I'm going to try a different approach that doesn't involve affecting this context menu.