I use a DIG 8006 set up like this:
http://www.plantedtank.net/forums/diy/126655-wasser-controller-2-0-complete-aquarium.htmlThis isn't my setup but I copied it and it is the brain of my tank. It runs my lights and ATO on a timer while giving me enough extra outlets for all pumps, heater, etc. I really love the set up and it cut down on the rats next of wires behind my tank.
It is really easy to set up. I use the 8006 controller because it gives the most features. Many allow more than one operation at a time but very few allow more than one operation and still allow you a 1 minute to 12 hour cycle.
Greg