Modal popups are evil!
I have been using early windowing systems, in particular the X-Windows system (with Xt/Athena Widget tools etc). These worked quite well, without resorting to modal popups. Then Windows started to spread, and with it, the usage of modal popups. I was immediately repelled by the restrictions these meant. Unfortunately, the usage of modal popups has spread outside of the Windows world, for example to Java, KDE, Gnome.
A modal popup prohibits the user from any interaction with the application, except for that popup window. This often feels like an insult to the user, who may have other ideas of what he wants to do with the program, and the order in which he wants to do it. In many cases, they simply constitute a usability catastrophe: Assume an error message, to which the user is expected to react ("cannot write file..."). In order to analyze the problem (why could the file not be written?), the user want to utilize other parts of the program, like the help facility. He can't. Because the modal popup is blocking the application. Or he want to look up "Error E6553-6633-995A2" in the documentation. Problem is that he has to destroy the information (contained in the modal popup) before he can access the documentation...
In some cases, modal popups are justified. (fatal errors, ending dialogs,...) In most cases not. The are just a way of unnecessarily restricting (and annoying) the user. In general, the more complex a program is, the harder it is for the programmer to anticipate the user's (sensible) wishes, and the more modal popups should be avoided.
So why are modal popups so widely used? Even by "Microsoft-criticals"? Possibly because people are used to being forced and do not question? Or because the programmers were lazy (It should also be said that using modal popups in some cases makes it easier to write correct programs; when limiting the user's choices, there is less that can go wrong...)
There is also an issue with program robustness: If a complex application somehow goes haywire, like generating "many" error popups, possibly in an infinite loop, the modal-popupper in general must be killed from the OS; a non-modal popupper can more easily be recovered.
The similarities between modal popups and DVDs UOP is striking: It is like disabling the Audio-key; "no need to use it, the user can go to the menu and there select his audio track".