In 616 he was Fury's best buddy and righthand man in SHIELD. Donning his trademark hat, "Dum Dum" Dugan would run the hardcore missions with Fury and get things done. I believe that him and Fury met in one of the wars and have been friends ever since.
I believe he may serve a bigger role in the Ultimate universe as Fury finds events to get out of control. (of course, assuming whatever it is in Nightmare ends up challenging Fury's mettle and ability to handle any threat)