<head runat="server">
<%
#if DEBUG
%>
<script src="jquery-1.3.2.js" type="text/javascript"></script>
<%
#else
%>
<script src="jquery-1.3.2.min.js" type="text/javascript"></script>
<%
#endif
%>
</head>
Works for me - note that this is based on the value of the debug
attribute in the <compilation>
element of the web.config.
Edit to respond to comment
Ah, so you're also adding controls to the head through the code-behind? Then you'll probably need to be adding this dynamically from the code-behind as well.
If you're happy to always serve the minified version, but want to use IntelliSense in Visual Studio you should ensure that you've installed the hotfix to enable this:
VS2008 SP1 Hotfix to Support "-vsdoc.js" IntelliSense Doc Files
This would enable you to name your non-minified version jquery-1.3.2.min-vsdoc.js and have VS read that one in while you're building the pages.