[robhack]

Minimize puts your window in the taskbar whereas X closes the window (not in the taskbar anymore), but whether it also closes the program or not at the same time is up to the program (and ideally should be configurable). That's how I understand it at least.

[jzzskijj]

BTW: In Skype 6.18.59.106 there is an option for "Keep Skype in the taskbar while I'm signed in." When it is unchecked, minimize and X behaves as you said.