The extra pins in the Micro end of the Nook USB cable are used to support the higher power draw of the Nook when charging at full rate (2.0A) since the max rated current of a Micro-USB connector is only 1.8A. I am sure they also use the additional pins to make the cable proprietary and possibly also control the bi-color LED. The extra pins are set further into the connector so that they do not cause compatibility problems with standard Micro-USB cables.
In addition to this, the charger brick that comes with the Nook has its Data lines shorted, to each other I believe, to indicate to the Nook that it is plugged into an adapter and not a computer.
The combination of those two things is what is needed for the Nook to charge at its full charge rate. Since the USB A end of the cable is a standard 4-pin design, extension cables that offer all 4 pins/wires will work fine.
The Apple adapter (even the 2.0A version) will not work because it uses a voltage divider (couple of resistors) on the data lines to indicate to the iPod/iPhone what style charger it is (1.0A or 2.0A). One of the data lines is held at 2.1V and the other at 2.7V. Depending on which one (D+ or D-) is at what voltage determines what style charger it is. So the Nook does not recognize the "non-zero" voltage values on the data lines and assumes it is a PC, so it will only charge at 500mA.
Other vendors power bricks use the same "short the data lines" trick as the Nook adapter so several others will work. I believe as mentioned already in this post that HTC uses this same method.
WARNING
Be careful though because if the adapter is rated at less than 2.0A (e.g. 1.0A) you could cause damage or fire. I am not sure if the Nook will slow down charging if it detects the charge voltage dropping if it is trying to pull too much power out of an underrated supply.
If you really want to use your Apple IPad adapter with your Nook Color/Tablet cable you could modify a USB A/A extension cable to disconnect the Data lines and then tie together only the data lines on the side of the cable that will go to the Nook. Again, this can be dangerous, I can not take any responsibility if you attempt to do this.
HTML:
USB A/A Extension Cable
[ ] GND ----------------------------------------------------- GND [ ]
[ ] D+ ------} <-tied to D- cut and taped-> D+ [ ]
[ Nook ] D- ------} <-tied to D+ cut and taped-> D- [ Adapter ]
[ ] +5V ----------------------------------------------------- +5V [ ]