Announced this morning on WebKit.org, the new version of Safari shipping with macOS Sierra this Fall is going to disable legacy plug-ins such as Flash, Java, Silverlight, and QuickTime by default.
From the WebKit blog post:
The WebKit project in particular emphasizes security, performance, and battery life when evaluating and implementing web standards. These standards now include most of the functionality needed to support rich media and interactive experiences that used to require legacy plug-ins like Adobe Flash. When Safari 10 ships this fall, by default, Safari will behave as though common legacy plug-ins on users’ Macs are not installed.



