I also encounter this problem three or four times per day.  I have three
monitors on two Nvidia Quadro FX cards, using the nvidia 177 binary
driver on 8.10.

I found that when the problem strikes, I can re-enable the mouse with the 
following steps:
1) Select a window using ALT+TAB.
2) Open the window's menu with ALT+SPACE.
3) Select 'Move' from the menu.  The cursor should change to the hand cursor 
and be positioned in the centre of the window.
4) Move the cursor with the mouse.  If this causes the window to move 
(unlikely), left-clicking should release the window and the mouse should work 
normally.
5) It's more likely that moving the mouse will just move the cursor and the 
window will stay put.  In this case use the cursor keys to move the window to 
the primary monitor.  If the window is already on the primary monitor, move it 
to another monitor, then back to the primary.
6) Once the window is on the primary monitor, move the cursor with the mouse.  
The window should move with the cursor, and mouse events register again.

This works for me every time.  It's far from ideal, and I detest this
kind of voodoo workaround, but it's better than restarting X.  Of
course, your mileage may vary.

-- 
X.org will stop responding to mouse clicks on Ibex with Xinerama.  Occurs 
frequently, Fatal Error.
https://bugs.launchpad.net/bugs/296167
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