It has been a Blender trademark that the user interface incorporated a non-overlapping window layout. Pre-2.5, it was impossible to move views so that they overlapped each other. This is no longer the case. Simply Shift+Click on the upper right of the view, and drag downwards and to the left. This will copy the view into an overlapping window, which can then be moved/scaled where ever you prefer.
Pros: You can have multiple overlapping windows if needed. This can be handy for running scripts in separate windows, or moving specific windows onto separate monitors.
Cons: Currently, there’s no way to keep a window on top while editing underneath. When you switch windows, the underlying window is forced to the top as the active window. You could use a hotkey to switch between the windows of an application (i.e. Mac OS X users can use Exposé to switch between the windows using F10, could be different depending on preferences).
Edit: I’m told there are some work-arounds for the overlapping windows to stay on top. They involve using the operating system’s window manager to do it. I don’t know of any way to do this in OS X, but I hear that linux users can do it. If someone knows, feel free to leave a comment about it.

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Nathan Letwory |
The use case for multiple windows is multiple monitors, not necessarily to have multiple windows in the same space to be on top of each other – the best thing to do is to still adher to the non-overlapping paradigm (even though you potentially can have windows on top of each other).
me |
You can change the level of the window to NSFloatingWindowLevel, or (better) use a NSPanel instead of a NSWindow and change isFloatingPanel.
If you change the level manually, you also need to monitor for the app losing focus or hiding, and then remove the floating level from the utility windows, as otherwise they will remain on top of all other windows which is annoying and bad. If you use the NSPanel class the system does that for you, another reason why it’s better to choose that route.
BrianH |
@me: Well, I meant for a way in Mac OS X on a non-coder level. I suppose a developer might be able to work it into the new window manager, but from what I read it looks like the overlapping windows are primarily for multiple monitor setups.
Egan |
At least on GNOME, there is an “always on top” button. I look forward to this feature not because I have multiple monitors, but because I have multiple virtual desktops.
Pustoolio |
On the Mac you can pop hidden windows to the front by Command + ` (the key below the escape key)