Sometimes you would like to create a virtual directory bellow for instance the SharePoint main site. Lets say you MOSS is installed at http://intranet and you would like to create your own virtual directory with your custom made aspx-pages at for instance http://intranet/custom. Well, if you use the IIS Management Console, add a virtual directory to the website, and add an aspx-page to that virtual directory, you will get errors saying that the application cannot find certain assemblies. This is due to the fact that these assemblies have been referenced in web.config using <add assembly="name-of-assembly" / > tags. Due to the way IIS works, these references are automatically inherited to all sub-directories, in this case, you virtual directory.
So, what to do? The simplest way to handle this is to add <remove assembly="name-of-assembly" / > tags to the web.config that resides in your virtual directory. This will explicitly remove the reference created by the parent website. Remove them one by one and soon you will be able to run your code just as you would like.
One good advantage of using adding your code to a virtual directory bellow the main site instead of using a new website at for instance another host header or TCP port, is that you can address your code using server relative urls. In essence, if you created an aspx-page at http://intranet/custom/mycustompage.aspx. If you address this page from the SharePoint, you can use the url: /custom/mycustompage.aspx without http:// or the servername. This also gives you the benefit that the page is on the same server, hence no security problems with IE.
In SharePoint, make sure that the address of your virtual directory is NOT bellow any wildcard included och explicitly included sites (in the setup of the webapplication in central admin).
Please note that adding virtual directories bellow the CRM root is an unsupported customization. This is due to the fact that Microsoft might release an update that adds a directory with the exact name of you virtual directory. This would give rise to either the fact that your code stops working or more likely that the content of the directory added by Microsoft cannot be accessed.