[desdiv]

The most mission critical one is probably the Aegis Ballistic Missile Defense System.

Here's Lockheed Martin announcing that they chose a (propriety) JVM to run "several critical subsystems" of the Aegis system in 2006[0].

Here's them announcing said project passing operational trials fours years later[1]. Surprisingly fast for a military project.

[0] http://www.atego.com/pressreleases/pressitem/lockheed-martin...

[1] http://www.atego.com/pressreleases/pressitem/aonix-perc-ultr...