All of a sudden once I hit 3000 miles on my 2006 coupe 6MT I started to hear a whining noise. I thought that I was being picky and that it wouldn't bother me, but now it's starting to get on my nerves. Here is my best description of the sound.

It sounds like a supercharger whining. The whine starts around 1,800 RPM and stays until about 4,600 RPM where I think the sound of the engine drowns it out. It happens with engine hot or cold. Does it with outside temperature hot or cold. Only does it under partial throttle in first and second and very faintly in third. As I accelerate the noise of the whining sounds speeds up. Does NOT make the sound coasting with the clutch pedal pressed in. Does NOT make the sounds when it is neutral and costing. Does NOT make the sounds if i rev the engine up when in neutral. Only happens when I am in a gear and under partial/normal acceleration. Under WOT I dont hear it but this might be because the exhaust drowns it out. It believe it is coming from the tranny.

Is this normal for our cars to make a bit of gear whine?

 

It actually sounds like your differential. I had a similar problem after my differential oil was replaced at the 30k service. I switched to a synthetic gear oil and that fixed the problem. Make use of your warranty and complain like hell.