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There's a couple of things at play here.
In neutral, at a stop light, you should be able to feel/hear the a/c compressor engage and disengage if you are using any HVAC setting where A/C is engaged. This will cause a slight fluctuation in RPM as the car's electronic throttle module compensates for the extra power needed. You may be able to feel it engage/disengage while driving, but that really depends on the car. I've never driven a manual V6. In some cars it's barely noticeable, and other cars, like in a Ford Focus, it feels like someone hitched up a trailer to the rear and you've lost 20hp.
If you're driving, and you clutch-in and let the RPM's fall, the RPM's should come back down to roughly idle speed. I too have observed in other vehicles, that the engine feels like it wants to die at the bottom of the RPM range. My only guess is that, in neutral, and 100% off the gas, while the vehile is at speed, the throttle cuts out. As the RPM's fall back to idle, the ECM wakes up and realizes the car is not in gear, and power has been cut, so it kicks on a little bit of power to keep the car idling. It's all momentary, so there's just a slight timeframe when the engine speed drops below idle, and then comes back up.
That's my best guess. I've had it happen in tons of other cars as well, so I don't think it's a problem, just how they're designed.
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