You have the source code so you can easily modify it to suit you custom needs if you wish. For example you can use the below script to to only make changes for certain roles:

Dim mUser As DotNetNuke.Entities.Users.UserInfo = DotNetNuke.Entities.Users.UserController.GetCurrentUserInfo
        If mUser.UserID < 1 Then
            'User not logged in so do something
        Else
            If mUser.IsSuperUser Or mUser.UserID = PortalSettings.AdministratorId.ToString Then
                'admin or host is logged in so do something
           Else
                'normal user is logged in so do something
            End If
        End If

Here are some other ideas that you can look at (especially the snapsis links) - http://www.dnncreative.com/Forum/tabid/88/forumid/4/postid/7783/view/topic/Default.aspx

If you have any suggestions let me know ;)

Rodney,
This adds AND subtracts files; CSSUnload only ...well.. unloads. 

Per portal, you could combine all the DNN core files into one optimized file and cut a ton of request and load time.  This also allows you to add jquery without having to enable widgets.  Further, you could replace MS AJAX with a CDN version for yet another performance boost.

Adam,
I use the Snapsis method now but it is a bit cumbersome.  I look forward to testing your suggestion.