Manual > Auto
1) When going down a hill in a low speed limit you need to be in maybe 3/4th gear (engine braking). You cant do this in a manual, you have to keep tapping the brake which is a pain in the arse.
2) Alert, you are much more alert when driving a manual, you have to constantly change gears, making you much more wary of your surroundings.
3) fuel consumption, Automatic consumes alot more fuel.
Found a couple links:
http://www.mouthshut.com/review/Automat ... 962-1.html
http://www.mouthshut.com/review/Automat ... 865-1.html