I have attempted to add two lines of code to the header portion of the default.aspx page.

head id="Head" runat="server"
    meta id="MetaRefresh" runat="Server" http-equiv="Refresh" name="Refresh" /
    meta id="MetaDescription" runat="Server" name="DESCRIPTION" /
    meta id="MetaKeywords" runat="Server" name="KEYWORDS" /
    meta id="MetaCopyright" runat="Server" name="COPYRIGHT" /
    meta id="MetaGenerator" runat="Server" name="GENERATOR" /
    meta id="MetaAuthor" runat="Server" name="AUTHOR" /
    meta name="RESOURCE-TYPE" content="DOCUMENT" /
    meta name="DISTRIBUTION" content="GLOBAL" /
    meta name="ROBOTS" content="INDEX, FOLLOW" /
    meta name="REVISIT-AFTER" content="1 DAYS" /
    meta name="RATING" content="GENERAL" /
    meta http-equiv="PAGE-ENTER" content="RevealTrans(Duration=0,Transition=1)" /    
    style type="text/css" id="StylePlaceholder" runat="server"/style  
    asp:placeholder id="CSS" runat="server" /
    script src="%= Page.ResolveUrl("js/jquerylatestpack.js") %" type="text/javascript"/script
    script src="%= Page.ResolveUrl("js/jquerypngfix.js") %" type="text/javascript"/script
    script type="text/javascript"
        $(document).ready(function() {                    
            $("img").pngFix();    
        });
    /script
/head

Note that i have removed the < > at the end of this example only so you can see exactly what i wrote.  There is a filter on this forum that prevents me from inserting script.

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>	An error has occurred. An error has occurred.

Which is not very meaningful to me.

I can't seem to find anywheres what is best practise to include JS files in my site similar to how you would a standard HTML file with the script link being defined in the portion of my HTML document.

Cheers.

The best way I've found to add javascript to a page is to include it in the "source" part of a Text/HTML module.

You can also add code to a skin file for something that you want on every page.

You can upload .js files and put them in the js directory, and refer to them.

Also, if you wish to add javascript directly into the default.aspx file, have a look here:
Incorporating sIFR (Scalable Inman Flash Replacement) with DotNetNuke skins

Scroll to the bottom - addendum for video 5 which demos how dnn incorporates javascript files.