In Meteor 2.3 deprecated flag has been introduced to packages so that package maintainers can tell people who use their packages or people who are looking at them that they have been deprecated and include a message. Until now all of that was limited to the meteor-tool and displays in console. Now you can get that information on Atmosphere as well!
There is a new red icon showing when a package is deprecated on a package box:
And on the package page itself you will get a message (if the author has set it up):