The Atom smoked a pipe in a panel of an issue of Brave and Bold. The artist, Jim Aparo, was a pipe smoker at the time, and he frequently drew pipe smokers in his stories, including himself. There's an issue of Superman where he tries pipe smoking and hated it (It was a "Private Life of Clark Kent" story, maybe the first one they did). I should also point out that Nick Fury never smoked a pipe in the comics, but Capt. Sawyer, who was his boss in WW2, did.
I hate to point this out, but Marvel, DC, and Archie Comics do not let their characters smoke anymore.