Changes
→Gnome
==Gnome==
From System->Preferences->Windows, check the option to "Select windows when the mouse moves over them", but uncheck the option to "Raise selected windows after an interval."
To unset click-to-raise,
* Press alt+f2 and type "gconf-editor".
* Navigate to apps->metacity-gGeneral.
* Uncheck raise_on_click. (A developer rant about how this functionality breaks the ideal GNOME interactions is present in the long description. The warning can be safely ignored. In the end, it is better to have the feature available with a long and opinionated caveat, than to have the feature yanked completely.)
==KDE==