it could be a million and one things. here are some things i would check out.

exhaust leak
cracked exhaust manifold or bad gasket
timing belt tensioner and belt itself
water pump
all accessory belts

if it does it when your in neutral have someone rev the car. get a long hollow metel pipe and put one end to your ear and the other end to the alternator, power steering pump if you have one, starter, throttle body, anything for that matter and see if you can isolate the whine. the pipe thing is an oldschool trick that acts like a set of stethacopes.