Just to add my own experience with the same problem:
My 06 MT is up to about 16K mi. I first started hearing this noise in the fall of last year after I had owned the car for a few months. At first it didn't happen all the time, but over the winter, it seems to happen almost continuously. There are still some times it does not happen, though.
I've had the dealer look at it on 4 separate ocassions, each time took it out with a technician and had them hear (and agree they heard) the noise. The first two times, they inspected everything and told me it all looked fine, and I didn't want them to drop the exhaust when the car was still pristine so I didn't ask them to try "fixing" it.
The third and fourth time I actually brought in PsyDoc's printout. They looked at the part, looked at my car, dropped the exhaust and agreed that what's going on is that under higher pressures, the pipe pushes down into the doughnut/gasket and rattles around because of how the parts come together there. (I realize this is a somewhat vague description, it was months ago and I have forgot some of the exact detail.) They agreed it didn't seem like it should make this noise but also said it didn't look like it was resulting in any problems. I got the impression it's sort of the purpose of that part to absorb this pushing.
On the fourth time they were all ready to fix the issue with that other part and were seeking approval from Acura to cover it under warranty. Acura came back and said they would not authorize it. Dealer was very apologetic, agreed they heard the noise, but couldn't fix it under warranty. They said again they don't think it's affecting the performance of the car (and I don't think so either) so I let it go and just stopped trying to fix it.
I'm not sure why some people seem not to hear it. I think it has a lot to do with the weather - temperature and humidity. That sounds a little crazy but I swear it's worse when things are wet, and when they're cold. On drier and warmer days, I don't hear it as much and sometimes not at all. I'm very curious to see if it goes away during the hot part of the summer.
Because the whole VTEC thing is one reason I bought the car and one of the things I really like about it, it's definitely a real gripe about a car I otherwise love almost completely. It's just that it sounds so *mean* above 6K rpm when it's not rattling, but so impotent when it does rattle.
You really can't hear it with the windows down, BTW.