I personally think that keeping the files separate during development is invaluable and that during production is when something like this counts. So I modified my deployment script in order to do that above.
I have a section that reads:
<Target Name="BeforeDeploy">
<ReadLinesFromFile File="%(JsFile.Identity)">
<Output TaskParameter="Lines" ItemName="JsLines"/>
</ReadLinesFromFile>
<WriteLinesToFile File="Scripts\all.js" Lines="@(JsLines)" Overwrite="true"/>
<Exec Command="java -jar tools\yuicompressor-2.4.2.jar Scripts\all.js -o Scripts\all-min.js"></Exec>
</Target>
And in my master page file I use:
if (HttpContext.Current.IsDebuggingEnabled)
{%>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/jquery-1.3.2.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/jquery-ui-1.7.2.min.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/jquery.form.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/jquery.metadata.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/jquery.validate.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/additional-methods.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/form-interaction.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/morevalidation.js")%>"></script>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/showdown.js") %>"></script>
<%
} else {%>
<script type="text/javascript" src="<%=Url.UrlLoadScript("~/Scripts/all-min.js")%>"></script>
<% } %>
The build script takes all the files in the section and combines them all together. Then I use YUI's minifier to get a minified version of the javascript. Because this is served by IIS, I would rather turn on compression in IIS to get gzip compression.
** Added **
My deployment script is an MSBuild script. I also use the excellent MSBuild community tasks (http://msbuildtasks.tigris.org/) to help deploy an application.
I'm not going to post my entire script file here, but here are some relevant lines to should demonstrate most of what it does.
The following section will run the build in asp.net compiler to copy the application over to the destination drive. (In a previous step I just run exec net use commands and map a network share drive).
<Target Name="Precompile" DependsOnTargets="build;remoteconnect;GetTime">
<MakeDir Directories="%(WebApplication.SharePath)\$(buildDate)" />
<Message Text="Precompiling Website to %(WebApplication.SharePath)\$(buildDate)" />
<AspNetCompiler
VirtualPath="/%(WebApplication.VirtualDirectoryPath)"
PhysicalPath="%(WebApplication.PhysicalPath)"
TargetPath="%(WebApplication.SharePath)\$(buildDate)"
Force="true"
Updateable="true"
Debug="$(Debug)"
/>
<Message Text="copying the correct configuration files over" />
<Exec Command="xcopy $(ConfigurationPath) %(WebApplication.SharePath)\$(buildDate) /S /E /Y" />
</Target>
After all of the solution projects are copied over I run this:
<Target Name="_deploy">
<Message Text="Removing Old Virtual Directory" />
<WebDirectoryDelete
VirtualDirectoryName="%(WebApplication.VirtualDirectoryPath)"
ServerName="$(IISServer)"
ContinueOnError="true"
Username="$(username)"
HostHeaderName="$(HostHeader)"
/>
<Message Text="Creating New Virtual Directory" />
<WebDirectoryCreate
VirtualDirectoryName="%(WebApplication.VirtualDirectoryPath)"
VirtualDirectoryPhysicalPath="%(WebApplication.IISPath)\$(buildDate)"
ServerName="$(IISServer)"
EnableDefaultDoc="true"
DefaultDoc="%(WebApplication.DefaultDocument)"
Username="$(username)"
HostHeaderName="$(HostHeader)"
/>
</Target>
That should be enough to get you started on automating deployment. I put all this stuff in a separate file called Aspnetdeploy.msbuild. I just msbuild /t:Target whenever I need to deploy to an environment.