I never see it coming, but it happens all the time: I go to minimize a Safari window down to the Dock, but the yellow button is grayed out. Hitting Apple-M doesn’t work, and “Minimize” isn’t available in the Window menu.
Well, it turns out to be a weird bug in Leopard’s window manager. If you’ve run into this yourself, let me guess: you have Spaces turned on, and you have something like VMware or Quicktime Player in full-screen mode in one of your spaces.
I can’t explain it any further than this. If you put an application in full-screen mode on one of your spaces, then use the arrow keys to switch to another space and back, the active application in the space you switch to will lose its minimize buttons. It happens in more than just Safari, but almost any application in the space you switch to.
The solution? Open yet another full-screen app, like Quicktime player, in the affected space. Simply switch to fullscreen mode, and then exit. The minimize buttons in the affected app will be restored.