TRY ADDING THIS TO YOUR SKIN FILE:

<script runat="server">
'SEE BLOG HERE: http://blogs.snapsis.com/CommentView,guid,eef98c82-f54d-480b-8e36-309ca6e406d8.aspx
Private Sub Page_Init(ByVal sender As System.Object, ByVal e As System.EventArgs) Handles MyBase.Init
Dim oCSS As Control = Me.Page.FindControl("CSS")
 If Not oCSS is Nothing Then

   'add a script reference for Javascript to the head section
   Dim oLink As New HtmlGenericControl("link")
  oLink.Attributes("rel") = "stylesheet"
  oLink.Attributes("type") = "text/css"
  oLink.Attributes("media") = "print"
  oLink.Attributes("href") = SkinPath & "print.css"
  oCSS.Controls.AddAt(0, oLink)
 
'to add another css style sheet uncomment the lines below
'  oLink = New HtmlGenericControl("link")
'  oLink.Attributes("rel") = "stylesheet"
'  oLink.Attributes("type") = "text/css"
'  oLink.Attributes("media") = "screen"
'  oLink.Attributes("href") = SkinPath & "screen.css"
'  oCSS.Controls.AddAt(0, oLink)

'to add javascript files uncomment the lines below
   oLink = New HtmlGenericControl("script")
   oLink.Attributes("language") = "javascript"
   oLink.Attributes("type") = "text/javascript"
   oLink.Attributes("src") = SkinPath & "extra.js"
   oCSS.Controls.AddAt(0, oLink)

'to add another javascript file uncomment the lines below
'   oLink.Attributes("src") = SkinPath & "sifr-config.js"
'   oCSS.Controls.AddAt(0, oLink)

  End if

End Sub
</script>

There is more than one way to "skin" this cat.

At Adski's suggestion, I looked at John Mitchell's technique for including custom .js files by defining them in your HTML skins.  This works well for JavaScripts but John suggests that you could also include .css files using a LINK tag.  The problem is that per XHTML, LINK tags must self-close.  John's technique will render but not validate.  Here is how I got both js and css includes AND without breaking XHTML rules.

I add this to the top of my HTML skin.

<script runat="server">
    Private Sub Page_Init(ByVal sender As System.Object, ByVal e As System.EventArgs) Handles MyBase.Init
       
        Dim header As Web.UI.HtmlControls.HtmlHead
        header = TryCast(Me.Page.Header, Web.UI.HtmlControls.HtmlHead)
       
        If header IsNot Nothing Then
            ' First CSS Include
            Dim oLink As New HtmlLink
            oLink.Attributes.Add("rel", "stylesheet")
            oLink.Attributes.Add("type", "text/css")
            oLink.Attributes.Add("media", "screen")
            oLink.Attributes.Add("href", SkinPath & "yui/build/reset-fonts-grids/reset-fonts-grids.css")
            header.Controls.Add(oLink)

            ' Second/Third/Etc CSS Include
            oLink = New HtmlLink
            oLink.Attributes.Add("rel", "stylesheet")
            oLink.Attributes.Add("type", "text/css")
            oLink.Attributes.Add("media", "screen")
            oLink.Attributes.Add("href", SkinPath & "yui/build/button/assets/skins/sam/button.css")
            header.Controls.Add(oLink)

            ' First JavaScript Include           
            Dim oScript As New HtmlGenericControl("script")
            oScript.Attributes("type") = "text/javascript"
            oScript.Attributes("src") = SkinPath & "yui/build/yahoo-dom-event/yahoo-dom-event.js"
            header.Controls.Add(oScript)
           
            ' Second/Third/Etc JavaScript Include
            oScript = New HtmlGenericControl("script")
            oScript.Attributes("type") = "text/javascript"
            oScript.Attributes("src") = SkinPath & "yui/build/animation/animation-min.js"
            header.Controls.Add(oScript)
        End If

    End Sub
</script>

Note that HtmlGenericControl will not self-close but HtmlLink will.  SCRIPT tags can close with </script> but LINK tags must self-close like <link />.  Thus you'll stay XHTML compliant.

I hope this helps someone else down the road.  Thanks to Adski and John Mitchell.

~ Garth