Now that most of the main newsreaders are able to handle it, I've made Atom the default format for HubMed XML feeds (example). The RSS version is still there at the same URL, and linked to from the Atom feed, for those tools that require it.
I couldn't use XML::Atom as this server doesn't have XML::LibXML installed properly (as far as I can tell - it works fine locally), so had to code it by hand - mostly based on Blogger's template, especially the nice CSS stylesheet. Hope they don't mind.