I wonder how the clipboard API could be fixed.
I suppose that the current scheme is that apps are monitoring paste events, and when it happens have a look at the clipboard for copied data.
Perhaps the clipboard shouldn't be visible at all, and only when the user decides to paste content should the targeted app receive a "paste" message with the copied data (or perhaps some more complicated selection mechanism with a list of recent copies à la emacs). This would essentially merge the 2 steps process outlined above into a single operation.
It's probably more complicated than that though.