Popup windows in Moodle cannot currently be styled separately from non-popup windows due to lack of a uniform body class identifying it as such (ex: #mod-resource-view and .mod-resource will modify all resources).
This is problematic when creating themes that are fixed-width and/or use margins or padding around the page or content. Popups appear fixed or padded in windows that do not support their size. A uniform class attached to all popups would really open the doors to theme development.
Moodle Themes discussion on this topic here: http://moodle.org/mod/forum/discuss.php?d=77000