This seems to be an issue that effects a few users (me included) and started at some point in OS X 10.6 Snow Leopard. Seems to be connected with Bluetooth failing to wake from sleep properly. The only 'fix' I've found that is 100% reliable is: System Preferences>Energy Saver and set 'computer sleep' to 'never'.
That's what I've been doing for the last 18 months or so, until the release of OS X 10.8.2. I've only had the problem a couple of times since then, so it looks like it's getting better but not fully fixed.
In fact, I had the problem yesterday for the first time in ages - keyboard/mouse or trackpad wouldn't wake the Mac. As an experiment, I plugged my iPod touch into a USB port and the Mac woke immediately .