one of my main complaints about Atom always has been that time as the primary key is pretty much hardwired into the format, and even though it is possible to use Atom for information where time is secondary, i think this part of Atom's design is a bit too limited in its scope.
since we are trying to use Atom (and AtomPub) in various scenarios where time is secondary or irrelevant, it is essential to be able to query feeds. there have been some ad hoc solutions, for example GData, which is not such a great design in various ways, including the idiosyncratic query format.
when searching for something else Atom-related, i ran into the Feed Item Query Language (FIQL), which is an approach to design a simple feed-oriented query language. i added that one to my Atom Landscape Overview and hope it will become successful. i definitely would like to see the language a bit more flexible (my main goal would be to be able to use it to use spatial queries on GeoRSS feeds), but it is a very good starting point.
the Atom and AtomPub landscape is getting more interesting every day, and while i am still waiting for the big wave of Atom(Pub) enthusiasm to catch on, it is definitely a very interesting ecosystem of formats and protocols that is slowly evolving.