You would declare your main jQuery scripts within the master page, as you would normally:
<head runat="server">
<link href="/Content/Interlude.css" rel="Stylesheet" type="text/css" />
<script type="text/javascript" src="/Scripts/jquery-1.3.2.min.js"></script>
<asp:ContentPlaceHolder ID="head" runat="server">
</asp:ContentPlaceHolder>
</head>
And then any page specific JS files could be loaded within the Content controls that reference the Head ContentPlaceholder.
However, a better option would be to look into the ScriptManager and ScriptManagerProxy controls - these can provide you with a lot more control over the way your JS files are served to the client.
So you would place a ScriptManager control in you master page, and add a reference to the jQuery core code in that:
<body>
<form id="form1" runat="server">
<asp:ScriptManager ID="ScriptManager1" runat="server">
<Scripts>
<asp:ScriptReference Path="/Scripts/jquery-1.3.2.min.js" />
</Scripts>
</asp:ScriptManager>
Then, in your page that requires some custom JS files, or a jQuery plugin, you can have:
<asp:Content ID="bodyContent" ContentPlaceholderID="body">
<asp:ScriptManagerProxy ID="ScriptManagerProxy1" runat="server">
<Scripts>
<asp:ScriptReference Path="/Scripts/jquery.fancybox-1.2.1.pack.js" />
</Scripts>
</asp:ScriptManagerProxy>
The ScriptManager allows you to do things like control where on the page scripts are rendered with LoadScriptsBeforeUI (or better yet, after by setting it to False).
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