September 11, 2001 was a tragedy to the World, the United States, and the cities of Washington DC, and New York. The West Wing, based in Washington, immediately came out with an episode, written by Aaron Sorkin, to enfold the events and the aftermath within the show's universe. Given that the show was a long-standing serial drama, that episode had a special drama that was clearly out of the normal flow.
[Law and Order, based in New York City, and filmed there, as I recall, never made a mention of the events of that day, either directly or indirectly, even though the show is episodic, and a mention or incorporation into the scripts would have been a less jarring effort.]
EDIT: This assertion is found to be inaccurate. There are quite a few direct and indirect references to the terrorist attack in the episodes here.
As in my other question about Serena Southerlyn, I am currently rewatching the episodes of that timeframe on Sundance, which is re-running the series "from the beginning". Knowing the real world event from that 2001 season, I am being especially concious to comments that might have a subtext. Being a given that the first few episodes were probably already in the can ready for the season premieres, it can be assumed the episodes say from 6 or higher through the end of season had a greater chance of such mention. Is there an episode or more that directly makes reference to the events in their city for September 11, 2001?