When you create a master page, you'll want to use some javascript expect core.js. You can find all of your js would be not load to your page if you put your js in server and using tag as follows:
How to use comstomizable javascipt file in master page?
You should put your js to C:\program files\common files\Microsoft shared\web server extensions\12\Template\layouts
and use code as follows:
<sharepoint:scriptlink language="javascript" name="../YourFolder in layouts/YourJS.js" runat="server"≯
