What are the differences between these two Java comet libraries? Is there a reason to pick one over the other?
From my personal experiences, i higly suggest you to get away from both of them! DWR team turned back to start development and version 3.0 will be ready soon.
From my own experience working with the Atmosphere framework it has some lack of documentation and issues too, like having to add your own functionality to the actual protocol. It is fairly recent and it seems to be gaining more traction and support but it (still) doesn't have a huge community behind it. Other than that it has both server and clients in Java and JavaScript. It's integrated in Vaadin framework and there are already many examples of use with other frameworks like Play and GWT. A very good thing about Atmosphere is that it virtually supports any container: Tomcat, JBoss, Jetty, Glassfish...so if this is a requirement it's a great choice.
Cometd I don't know from experience but what I know from looking around is that it seems to be very well documented. The GH repository doesn't have as many followers as Atmosphere though. From what I know it doesn't support as many containers as Atmosphere.
Both integrate with Google Guice and other common requirements.
You can also find an old article on this question here, but both frameworks evolved a lot since then:
http://www.ibm.com/developerworks/library/wa-reverseajax4/
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