Multi windowed mode with Gimp the 'small windows' should follow the main
window up and down in the windows hierarchy. Either your experiences are
not with recent Gimp versions or your window manager sucks and you should
use a different one.
That should be the default behavior for Gimp 2.6. The 'daughter' windows are hinted as 'utility windows' to the Window manager and they should follow and bring up the other windows.
In earlier versions this was not the default, I think, but you could configure it to make all the windows behave in that manner.
With the current development version of Gimp they added a 'one window mode' so that it'll reflect the Photoshop behavior in Windows.
Note that in OS X each application has it's own virtual desktop, more or less. Each has their own plane of existence and the main menu bar is always the same place no matter what your window placement is... right there at the top of the screen.
Like if your using a browser with lots of browser windows open. When you click on one of the windows it brings up _all_ the windows for that application.
So Photoshop in OS X is much more like Gimp in Linux rather then Photoshop in Windows in the way the window management works. It's just that in Linux you would have to manually separate your Windows into each virtual desktop rather then have it happen naturally; which makes it all very confusing for people not used to how the Linux desktop works. In comparison people are able to use OS X's multiple desktops without even thinking about it since they are all visible at once because they are layered on top of one another.
With composited desktops it should now be technically possible for Linux to emulate the intuitive window management that OS X uses. (Unfortunately all that people seem to want is to get OS X's dock... which is horrible beyond all words. The 'dock' is the worst feature of OS X's desktop IMO. It looks cool, but it's just kinda fails in practice)
I am hoping that in Gnome 3.x stuff they will introduce a way to automatically group application windows and such together on their own desktop. That would be a terrific feature to have. That way you could get rid of the need for 'tabs' in most applications. I like it in my browser, but hate it in my gnome-terminal.
Plus it would make tiling make much more sense, which is a great feature for some window managers, but requires a lot of manual manipulation or scripting to pull off.
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