If it's only when the throttle is partially pressed, it could very well be your TB. As-in nothing is wrong. If you put on an aftermarket intake, this is the "intake whistle" that people talk about. The intakes do NOT give you the whistle, they DO remove the BMW baffling that hides most of it. Even putting in a drop-in filter is enough to reveal it. Some E46s do it more than others. I noticed that at lower elevations my car whistled less so air density MIGHT have something to do with it. If you shut the engine off and listen carefully very soon after shutting it off, do you hear a clink/ka-*****/metallic sound? Does it sound similar? If it's just your TB whistling then it should have a similar sound quality to it.
The CCV is indeed a nightmare. When your engine is idling, pull the dipstick out. Is Chewbacca hiding in your engine? If no, your CCV is probably fine for now. Also the CCV usually fails in the cold, not the early summer.
I spent two months chasing that whistle. Even did a 10PSI smoke test. Nada. Sealed tighter than a pickle jar. Then I read a post from waaaaay back when the E46 was new of people complaining about the whistle and it was normal.
Here's a video I did of the Injen intake noise since someone requested it. Listen very closely starting at 6 seconds right as the engine begins to rev. Do you hear your whistle?