I discovered this by accident, but my life has been measurably better since.
You probably already know that you can switch apps quickly with Cmd+tab. But if you reach your pinky up a bit more and hit Cmd+~ you can rotate through the windows of the current app. This turns out to be most useful when, say, your email compose window gets behind the main email client window.
What is the equivalent keystroke on Linux? -m
This isn’t an issue in Linux b/c each application window can be Alt+TABed to. Others would probably argue focus-follows-mouse also solves the problem, which I actually found to be helpful working with the Gimp.
Either way, I couldn’t even start working on OS X until I found that shortcut.
I made sure to research that one before even switching to the Mac. Alt-tab is for me the single most important user-facing feature of any OS. And I am only half joking. Really, it is. :)