One of the old school method of building build custom web application on top of SharePoint Portal is to deploy the web application within SharePoint’s web application. Most oftenly, the _layouts folder is used. I do have to note that this might not be the best way to do it, but it’s the most straight forward way.
With CMS now part of SharePoint in MOSS 2007, there is an additional step required: the PublishingHttpModule need to be explicitly removed from the _layouts folder. If this is not done so, the custom application will not work properly. The web.config file in the wss virtual directory need to include the following settings within the <configuration> section:
<configuration>
<location path="_layouts">
<system.web>
<httpModules>
<remove name="PublishingHttpModule" />
</httpModules>
</system.web>
</location>
</configuration>
SideNote: I’ve almost forgotten about this setting until a colleague of mine bumped into this same issue, which already happened to me earlier this year when I haven’t started blogging yet. I would credit this finding to some resource on the web but unfortunately I don’t recall where I found this info from already. Anyway, belated thanx, whoever your are...