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I'm from a Linux background trying to get used to the differences with Mac OS X. I've gotten resigned to the fact that to switch from one window to another I first need to switch Apps via CMD+Tab and then windows via CMD+`. This isn't too much of a problem as the majority of my windows are under X11 anyway.

However, there's a big annoyance with the window-switching (which, as far as I can tell, doesn't happen with the app-switching). When cycling through the open windows, each one is brought to the fore as I cycle past it. So if I have a dozen or so windows open in X11 and want to continually switch between two of them, it's next to impossible due to the fact that every window gets raised as I cycle between the two that I want (moreover, there's no intelligent ordering: the cycling goes on what appears to be launch-time rather than last-access-time which would be more sensible).

Is there any way to fix this so that window-cycling only raises the one that I want and not all the ones I have to step over on the way?

I don't mind if the fix is only for X11 (I'm using XQuartz, in case that's relevant, and am still on Lion).

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To continually switch between two windows use Command` and, to go back to the previous window, ShiftCommand`. I tested it with XQuartz and worked as expected.

Otherwise: Can't you select the window you wish to bring to the front from XQuartz's Window menu?

Other possibility is to use Hot Corners (introduced in OS X 10.3 "Panther") to show all application windows, then choose the one you need. There are plenty of guides out there, for instance http://heresthethingblog.com/2012/02/06/mac-tip-control-desktop-hot-corners/.

Basically (in 10.7 "Lion" and later), you have to open System Preferences, select Mission Control and press the button Hot Corners... in the bottom. Then you can select a corner for action Application Windows.

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Just as a side note "hot corners" was introduced in 10.5 Leopard. –  soxman Nov 17 '12 at 5:05
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It was introduced even earlier, in Mac OS X 10.3 "Panther". I've corrected my answer, thanks for mentioning it. –  jaume Nov 18 '12 at 9:49
    
+1 Totally true; I was thinking of "spaces". –  soxman Nov 18 '12 at 17:17
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