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1b1ed1a
(Get the code!)
I was running Vinagre (gtk vnc client) which appears to do some kind of input stealing when its vnc widget has focus.
I suspended my laptop and on resume keyboard input was working, the mouse pointer moved (and pointers updated in the right places, e.g. window borders showed a resize pointer), but X apps were not able to see pointer motion events or mouse buttons.
restarting hal, rmmoding, changing VTs, etc. were not able to restore normal behaviour.
xinput test was seeing motion and button events.
locking the screen with gnome screensaver and then unlocking, returned things to normal.
Presumably X was still under the impression that something was grabbing mouse events even though I had killed vinagre from a console (but before killing it, things had already gone wrong).