The Synergy Project, a program that allows cross-platform sharing of keyboard and mouse, has released version 1.6.3, which has a potentially really important fix in the changelog:
1.6.3 ===== Bug #4349 - Mouse click does not always bring window to front
I’ve been having a lot of problems with Z-order on my desktops, and this may be the problem. I haven’t done enough triage to definitely say, because Synergy is so useful that I’ve not really been willing to consider not using it; the alternatives are just not good enough.
If you use Synergy, definitely get this update. If you don’t, and you have multiple machines on your desk and want to share the keyboard and mouse, try Synergy. If you’re Mac-only, my Mac friends tell me Teleport is the bee’s knees; I’m not Mac-only, and Synergy has totally rocked for me.