If you, too, think click-through is inconsistent and annoying, Klicko will be useful.
Klicko is a System Preferences panel written in Cocoa. It doesn't hack the system, other applications, inject code or do anything magic. Now you must first click anywhere inside a background window to bring it to the front.
Klicko also has two other convenient functions: window maximizing and bringing all windows of some application to the front at once.
* Klicko can be instructed to not act on any of a list of applications, or
* Klicko can act only on specific applications in a list.
* Klicko can make a window's Zoom button maximize the window to the full screen.
* Bring all windows of an application forward by control-option-command-clicking on any of them; this also lets you bring all Finder windows forward by control-option-command-clicking on the desktop.
* Klicko will momentarily let through any clicks with a modifier key.