We have a 2005, I know, different models,etc. BUT, we have a roof rack with crossbars. With the sunroof open there was a humming, whistle, vibration noise. We took the crossbars off and the sound went away.With my old 4Runner, if the sunroof was open I would get a vibrating sound from the passenger seat belt. Snapping it shut solved that problem.
Now with my Outback (2.5 PZEV CVT), I've noticed that when I'm going 20 to 40 MPH or so, with the sunroof wide open, and it's quiet in the car (no radio, no wife), that there's a vibration/humming sound coming from the interior. Fairly high frequency (more of a treble sound than a bass), and I'm sure it's just some fabric or something going harmonic on me, but I can't for the life of me find it.
This happens when the roof is all the way open from the one touch open, and when the roof is open that extra inch from pushing the button again (secondary question: why do they have that "feature"?).