As has been noted here Sci-Fi, USA and Bravo carried their regular programming. I agree if NBC would have owned them back in 2001 NBC would have preempted those channels with NBC News and MSNBC and even local coverage from WNBC-TV.
Which reminds me, VH1 carried coverage from WCBS-TV for many hours on that day.
Comedy Central ran a scroll at the bottom of their screen urging viewers to donate to The Red Cross.
I seem to recall most, or all, of the ESPN channels carried ABC News. Later in the evening ESPN's SportsCenter had a special program about that day.
Now that I think about it, WWOR, of all channels, just aired coverage during their regular newscast. Does anyone know if this was on their national feed, or if it was like this on their New York OTA signal? After all it seems very odd an event of this proportion and magnitude would go unnoticed by a New York television station, even if it is a second tier superstation.
Even WGN's national feed had continuing coverage for about two days; giving the nation coverage from WGN News and at (many) times feeding New York's WPIX's coverage to the nation.
All the movie channels carried on as normal and I don't seem to recall stations like HBO and Cinemax running some type of scroll at the bottom of the screen.
Here in L.A. our main PBS station, KCET, carried the morning and afternoon children's programs with a scroll running along the screen urging viewers to tune in later in the evening for a special edition of "The News Hour." Our second tier PBS station, KLCS, was airing coverage from BBC News.