So we have these big JavaScript functions in one of our MasterPages. I wanted to move them to a separate file but it proved more difficult than I thought!

I could not add a <link> or <script> tag to the get and use an application relative path such as ~/Scripts/MyScript.js".

Ended up just creating the control dynamically but it was interesting how I had to arrive to the right path. Here it is:

// Retrieve Header
HtmlHead header = (this.Page.Header as HtmlHead);

// If we have access of the page header:
if (header != null)
{
    // Add script block for Master functions:
    HtmlGenericControl scrptBlck = new HtmlGenericControl("script");
    scrptBlck.Attributes.Add("src",
        VirtualPathUtility.MakeRelative(
                Request.AppRelativeCurrentExecutionFilePath,
                "~/Scripts/MasterFunctions.js"));
    scrptBlck.Attributes.Add("type", "text/javascript");
    header.Controls.Add(scrptBlck);
}