And here I thought Zwoptex, and that’s going to be it in terms of Texture Atlas creation. Much to my surprise I found the TexturePacker tool. But in comparison to Zwoptex, it doesn’t have a GUI, it’s a command line utility. On the other hand, it does everything automatically and is probably going to be a great choice for any automated procession. It can output in both Cocos2D and Corona formats.
The TexturePacker is available from the code’n’web website and costs around $15 (€10).
It has a few very interesting features, for example removal of duplicate images and color reduction. Check out the feature comparison chart on the Cocos2D wiki.