After upgrading to WSS 3.0 I noticed that I no longer could exclude managed paths for directories that you don't want 'managed' by SharePoint. So how do you do this then? The answer is simple, you don’t have to do anything. Just create your virtual directory in IIS and that's it. WSS will just ignore it.
One extra thing to remember: don’t forget to perform an IISRESET, otherwise SharePoint isn't yet aware of the new mapping.