The Scout Commander can be found immediately following the first boss in Realm of the Fae. He comes with ~20 archer type adds. Stay back after killing the first boss and let the Commander and his flunkies spawn. Focus all of the groups DPS on the adds before dealing with the Commander.
The Mage Commander will spawn after the second boss is defeated. His mages will surround the nearby pools. When the group is ready quickly handle his mage disciples and then dispatch him.
The Troop Commander will spawn as soon as the third boss is slain. His troops will make a large circle surrounding the area that the boss stood in. When engaged they will run into melee range so AoE'ing them is very easy. Stay grouped up and quickly eliminate them. The Commander will fall shortly after.