Focus-follows-mouse (plus auto-raise) on Mac OS X
You can do it for Terminal.app by issuing the following command at the command line:
defaults write com.apple.Terminal FocusFollowsMouse -bool true
For X11 apps you can do this:
defaults write com.apple.x11 wm_ffm -bool true
In Snow Leopard, use this instead:
defaults write org.x.X11 wm_ffm -bool true
Apparently there's a program called CodeTek Virtual Desktop that'll emulate it systemwide, but it costs $$ (and they never got a version out for OSX Leopard).
Steve Yegge wrote an essay about this a while back, where he tried and failed to write a suitable extension. I've since tried to find focus-follows-mouse applications for OS X and failed also.
Although this is far from a complete solution, two handy actions that are built into OSX (10.11) are:
⌃⌥-click (control-option-click) - switches focus without raising window
⌘-click (command-click) - clicks in window without switching focus
Not sure when these shortcuts were introduced, as I haven't been able to find them written about anywhere.