Jason Snell reveals:

Fans of the yellow button, fear not: by default, Snow Leopard still minimizes windows the same stupid way Mac OS X has for the last ten years. For us complainers, though, there’s a new alternative: A Minimize Windows Into Application Icon checkbox in System Preferences’ Dock pane. With that box checked, when you click on that yellow button, your window will still fly away into the Dock. But instead of disappearing into the mess on the right, it will minimize into the icon of the application it belongs to. That makes it easy to bring the window back. (Minimized windows are indicated in most programs by a diamond in an app’s Window menu; you can see that same list by Control-clicking on the app’s icon in the Dock.) Even better, this feature works with Exposé: When you invoke Exposé, all minimized windows line up together at the very bottom of the screen.