Take 2 content place holder in master.
<head id="Head1" runat="server">
<asp:contentplaceholder id="head" runat="server" xmlns:asp="#unknown">
</asp:contentplaceholder>
</head>
<body>
<asp:contentplaceholder id="Main" runat="server" xmlns:asp="#unknown"></asp:contentplaceholder>
</body>
In Head tag you can include common script files and css.
If you wants to include any script in child page, than you can include within "Head1" Content place holder.