Abdera + JCR = Atom server?
Like several other people I think Atom and JCR are made to collaborate.
I just had a look at the JCR CollectionProvider that Dan Diephouse created for Abdera, and it's cool stuff! The Test code shows how easy it is to setup Abdera to use a JCR Repository for storage.
Having APP besides WebDAV as an access protocol for JCR repositories would be great. JCR semantics are richer than both of these protocols, but having multiple content access and manipulation methods accessing the same storage is very helpful in many cases.