How do I cycle through windows without bringing each to the fore? 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).
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.