Klicko

Klicko is a straightforward application that essentially restricts click-through in inactive windows while it's running. It doesn't tamper with any other applications nor does it inject any code to perform its function. The standard action for clicking an inactive window will merely bring it and its corresponding application to the front. However, there may be some limitations when dealing with applications utilizing non-standard windows.

In case you need to temporarily enable click-through, simply hold down any modifier key while clicking. You also have the option to permanently include or exclude specific applications in the Preferences.