When using keyboard shortcuts to cycle between multiple open windows (⌘+`), only the most recent two windows are cycled. I generally have multiple windows open at a time, and would like to cycle between all of them.
That's funny, I submitted a bug report about this issue earlier today (Key: VB-13169).
As a temporary workaround, you can press shift in addition to the keyboard shortcut which will cause you to cycle through windows in reverse chronological order and that is not affected by the bug. It does feel a little clumsy, though, which is why I have used Keyboard Maestro to send the shortcut version with shift if I press the regular shortcut and vice versa.
Btw, the shortcut to cycle through windows differs by keyboard layout (e.g., on my machine it's ⌘+<). Anyone unsure of the shortcut on their system can look it up at: "System Preferences->Keyboard->Move focus to next window"