@eemceebee
For loading, I actually meant loading the saved XML file and atlas map into your cocos2d app, not loading XML back into the tool. I agree that it's best to just rely on the algorithm!
The smartCrop feature sounds helpful. zwoptex crops your images too, but importantly, it remembers offsets for where the images were cropped. This is really important when you have layered animations that need to align properly when you load them! In this case, the images you import often have transparency around them, but this is on purpose so they line up with other layers.
By the way, if you use Photoshop, you can use Image | Trim... to easily remove all transparent pixels from the edge of your icons!