Nintendo of Japan have confirmed that Metroid NES will be coming to the 3DS as part of their Virtual Console lineup. The game will be available to all before the year is out but Nintendo Ambassadors, who bought the 3DS before the price drop on August 12th 2011 will be able to download the game completely free. It joins Metroid II: Return of Samus and Metroid: Fusion (Ambassadors only) on the 3DS before the year is out.
UPDATE: Nintendo of America has updated their 3DS Ambassador page to confirm that the region will be receiving the same ten games as Japan. Still waiting on confirmation for Europe and Australia/New Zealand.
Source: Nintendo Japan