A couple of ongoing fictional series' have indirectly taken on the War on Terror as a subject for drama. The new Battlestar Galactica and Marvel comics Civil War certainly try. One of the most appropriate works which takes on the issues of the war is the Japanese manga turned anime Full Metal Alchemist.
If you don't like anime and you want to see what I'm talking about, you should skip ahead to 6:40.
Even without any political overtones, Full Metal Alchemist reaches the top of the anime pyramid as it alternates between comedic and dramatic, lighthearted and deep in contemplation of the darkness of the soul. It does get a bit long winded and plot twisty in the middle of the series though. Leave it to Japan to understand what it means to be a dominant colonial power as well as a satellite state.