Will the Airport Extreme card from the 2006 Mac Pro work in the 2008 Mac Pro?
Yes it will! Just tried it with success! 

My largest indicator that it would work was by reviewing high reputation eBay sellers who where selling similar cards and claiming a wide range of Mac Pros. 

Successfully transfered the Airport Extreme Card from the Mac Pro 2006 in to a Mac Pro 2008

I have the following Airport Extreme Card that identifies itself in System Information as :

Card Type:         AirPort Extreme  (0x14E4, 0x8C)
Firmware Version:  Broadcom BCM43xx 1.0 (5.10.131.36.11)


The card as pictured is:


Installation Note:  There were 3 wires to choose from inside the Mac Pro (Both models), labeled 1,2,3.  The longest one I thought was for the Bluetooth module, clearly not the case in the Mac Pro 2008. Anyways, I connected the shortest wire to the top antenna port and the middle length to the lower antenna port on the Airport Extreme Card. Test working great, with this configuration and logic. This is the same logic I used when I initially installed the card in the 2006 Mac Pro as well. Not really sure what the long length cable is for as pictured below. 

I would assume this would be for a true 802.11n card since those had 3 antennas in their spec?