If you try using PHP & jQuery image upload and crop [http://www.webmotionuk.co.uk/php-jquery-image-upload-and-crop/]
with some sort of modal like popup functionality, you will notice that the imgareaselect selection does not have proper zindex value,
although this plugin is using 0.6 version and 0.8/0.9 claims to have added zindex option, still doesnt seem to work

so grab 0.6 from link above and change the following line in the .js file

$a.add($o).css({ display: ‘none’, position: fixed ? ‘fixed’ : ‘absolute’, overflow: ‘hidden’,
zIndex: zIndex > 0 ? zIndex : null });

to

$a.add($o).css({ display: ‘none’, position:’fixed’ : ‘absolute’, overflow: ‘hidden’,
zIndex: ‘999′ });