I've just installed yakuake in kubuntu 11.10, but cannot see it in the "Custom Shortcuts" settings.
How to change shortcut to win+~ in this case?
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You can still configure the Global shortcut in the application itself.
Launch yakuake. In its menu (In my theme the little triangle between "pin" and "close" at the lower right corner) you will be able to select the entry "Configure Shortcut..."
Here you will be able to select your preferred Shortcut in the Global column (by default F12 key)
Same for other KDE applications, as far as I seen, you can select the global Shortcut from the application itself.