Tim Bray writes about zapping Doctype. Amen to that. Here is a posting from 2001 where I outlined my reasoning for not using it. For a while I remember signing myself as Sean "deprecate doctype" McGrath on xml-dev:-)
Oh, and here is a spec for an XML 1.0 profile that works around the interop and processing issues created by doctype. It has changed somewhat since I was involved but the core concepts remain the same.