5906 has a longer barrel and grip frame. 5906 guns have stainless steel frames and slides. Capacity is 14 or 15 depending on the mags.
6906 is the compact version of the 5906 guns with an added twist. The frame is aluminum. Capacity is 12 or 13 depending upon the mags (apparently there were some changes later on that increased the capacity).
The general rule with S&W 3rd generation autos is that the "6" in the last digit denotes a stainless steel frame while a "3" means aluminum frame. In the case of the 6906, this convention doesn't hold (AFAIK this is the only exception in the S&W line). 6906s are excellent carry guns, BTW.