I used to try closing the pop boxes with javascript after the user completed the form and submitted it. but when some people used pop blocker, it redirected the main window to the pop up url and then when the user submitted the form it would close them out of their browser (after prompting them"the browser window you are using is trying to close...")
I also would refresh the parent window after some input like adding an invitee to a party invite list. That would fail if they were not in a pop up window.
Another issue with safari is that the window.close script i was using would not close the window - they would have to do it manually.
There are also formatting issues because ie/netscape/safari all interpret classes applied to form boxes differently. so if I opened a pop window with no scrollbars or nav buttons, people could not see the submit button, or the input items that flowed beyond the window dimensions. because the size of the form elements are all different depending on the browser.
These are just a few of the issues, so I decided to start building everything without using pop ups.
The more I develop websites, the more I lean toward simplistic interfaces.