When Mac OS 10.5 Leopard was released, I eagerly tried using Spaces, and assigned several apps to different windows. After a while, I disabled Spaces as I just didn't use it that much.

Then I noticed that sometimes application windows would vanish, and even if I selected them from the Window menu, they would not reappear -- similar to what is discussed in this hint, except in my case, Spaces was disabled. This is due to a known Spaces bug.

I realized that to prevent this from recurring, I just had to re-enable Spaces temporarily, empty the list of applications with assigned windows, and then disable Spaces. Perhaps obvious, but perhaps useful to somebody.