After having this drive me crazy for a while, I found others that were having the problem on Apple's forums. The symptoms are 1) 2012 Mac Mini 2) Fresh Upgrade to Yosemite 3) After being asleep for a while, waking the machine glitches out. Specifically, you can move the mouse, but that's it. The time is frozen, you can't launch or quit apps. It turns out that it's a glitch in the audio driver. While everyone waits for a patch, the fix is to either unplug your speakers entirely, or to plug them into a monitor that's getting a HDMI feed if it supports that. Alternatively, run your monitor over another cable that isn't HDMI. The core of the problem is having two audio interfaces seen on the Mini when it wakes up.