This ability to manage every aspect of every open window from the keyboard--to minimize windows, maximize them, restore them, resize them, move them, maximize them in just one dimension ("maximize vertically"--surprisingly useful), and pop them from one virtual screen to the next--is built into just about every open-source X window manager written by obsessive lunatics and given away for free. It should be built into this gold-plated and otherwise wonderful implementation of Unix-for-the-desktop as well. Yes, you can probably do two-thirds of these things from the keyboard, sometimes, if you're willing to hit cmd-F2 and laboriously scroll rightward across the menu bar. But that's silly. And meanwhile, while you can generally minimize a window with cmd-M, is there a similar keystroke for getting that minimized window back up out of the Dock?
I love OS X, but it's kind of pathetic that every so often I find myself starting XDarwin in fullscreen mode just to have another virtual desktop--or firing it up rootlessly just so I can have some xterms I can move around the screen at need, without having to constantly grab the damn mouse.
Speaking of rootlessly, I'm a little surprised nobody seems to have mentioned OroborosX, an X window manager specifically designed to run rootlessly under OS X. It's a bit of a CPU hog and it's sufficiently Mac-like to suffer from exactly the keyboard deficiencies I'm griping about above, but for some kinds of work it's exactly the right thing. Usually, though, I just run icewm.
A discussion question, and then I'll stop. What Classic utilities are you still wedded to, this far along? (My own submission would be the unkillable Disktop, a ten-year-old copy of which is as solid and useful on this OS X machine as it was on the Mac my wife and I shared ten years ago.)