I seems obvious to me that Atom Feed and Entry docs are potentially quite different things which can be used for entirely different purposes. The contention that an Entry doc is somehow really the same as a one-entry Feed doc is entirely unconvincing.
The Architecture of the Web (http://www.w3.org/TR/webarch) and the TAG finding on Authoritative Metadata (http://www.w3.org/2001/tag/doc/mime-respect.html) make it pretty clear that it's advantageous to use HTTP headers to distinguish between different kinds of representations.
So I guess I'm in favor of us writing something down to address this problem.
RFC4287 is now pretty widely implemented, so there is a distinct cost to screwing around with the well-known application/atom+xml. On the other hand, my perception is that virtually all software that knows about 4287 knows about feeds, rather than entries. Thus, it seems to me that introducing a parameter so that existing software might see application/atom+xml;type=feed *might* break some software. But introducing a new media-type application/atom-entry+xml which only goes with standalone feed documents is very unlikely to break anything.
So I'm for James' option B) application/atom-entry+xml (James, did you really mean "atom.entry" with the ugly dot?) -Tim