Bluetooth was turned on to my surprise (I never use it), but disabling it did not fix my problem: Siri doesn't hear me through the phone mic, only the iPhone headphones microphone. So far it seems that the mic works fine during all types of phone calls, just not when Siri is activated for some reason.
I have a 16g 4S and intermittently people can't hear me when I make a call. If I activate the speaker then they hear me fine. I'm guessing there's only one mic and since it works with the speaker the mic is probably ok. Since the mic is likely ok I think Apple has a bug in their firmware someplace. I think I've noticed this only happens after I undock the phone from my Apple docking thing (just for power and input to a stereo). I bet it's related to undocking the phone.
There are actually two microphones: the standard mic is on the bottom next to the 30-pin dock connector, and the other microphone (activated for FaceTime calls and when you use speakerphone during a phone call) is located on the top of the device next to the headphone jack (tiny little pin-hole).
When my standard mic stopped working, I tried everything, including erase/restore, then called AppleCare (within my 1-year factory warranty) and they overnighted me a replacement phone for $29. Others have been having microphone problems since the iPhone 4, and it seems (at least for the standard mic) that there is no easy fix.