In general it is better for the perfomance of your website if you add JS links at the bottom of the page.

But if you want to add stuff to the head of the page you can do this like this:

<script runat="server">

    Private Sub Page_Init(ByVal sender As System.Object, ByVal e As System.EventArgs) Handles MyBase.Init
        'add a script reference for Javascript to the head section
        Dim oLink As New HtmlGenericControl("script")
        oLink.Attributes("language") = "javascript"
        oLink.Attributes("type") = "text/javascript"
        oLink.Attributes("src") = SkinPath & "js/" & "my.js"
        Dim oCSS As Control = Me.Page.FindControl("CSS")
        If Not oCSS Is Nothing Then
            oCSS.Controls.AddAt(0, oLink)
        End If
    End Sub

</script>