Digging into the schematics for the Cubieboard tonight and focused on the power management IC. It is an AXP209, which has an integrated push on/off function which is controlled through linux. In fact, the power switch on the board is just a push button. So nothing special needed for this.
The AXP209 also has a lithium ion charger built in, as well as outputs to control point of load supplies to peripherals. These don't appear to be used, but hacking into these may be useful to shut down the supplies to the hard drive and USB hubs.
The datasheet is in Chinese and my Chinese is a bit rusty (ok, it's non-existant.) But I am determined now to figure it out.
There is plenty of English information at the link below, however.