An app developed by another team here at Acme Software overrides - in fact, erases - the operating system-provided system menu (it also custom paints the minimize, maximize, and close button, but that's another issue). My opinion is that this is a bad idea; it interferes with deeply-ingrained user expectations. For example, you cannot double-click the top-left corner of the window to close the app; it maximizes instead.
Is there a valid use case for overriding the default appearance or behavior of the OS system menu? Are there good arguments for or against?
Here's an example of a slightly modified system menu which, IMHO, is acceptable:
Browsers work hard to minimize wasted space; they're intended to fall into the background and let you get on with what's below. Also, while clicking on Opera's replacement file menu does not give you the standard Move, Size, Minimize, and Maximize, hitting Alt-Space brings up a conventional menu with all of those, so keyboard users are not hindered.