Mystery noises can be hard to diagnose. Look at it this way; your car has 90k miles and is almost 9 years old. No matter how much you babied the thing, eventually some indicators of the car not being brand new will arise. Is it reasonable to expect that your car is going to sound just as it did when it was new?
You said it runs smoothly otherwise. Mine is a 04 and has 87k miles on it. It also has some weird noise that I hear at idle (which is also quite rough sometimes) coming from the vents. But when I drive the thing, it's smooth, responsive and generally quite good.