Hmm, I dont know if it would count, since it's AU, but Infrangible Road has a section that addresses that. I reccomend reading it, it's a lovely story.
Big Pnk's utterly brilliant fic 'Fire in the hole' has a section that has John and Dean at Shanksville, Pa on Sept 11. I can't recommend her fic enough.
The only 9/11 fic I've read is by ficwriter1966 entitled 'Driftwood' http://ficwriter1966.livejournal.com/38193.html
This is an awesome fic. The Winchesters are on the East coast and John isn't with Dean or Sam when it happens and they fear the worst. Highly recommend this one.