Nerve Gas 9/11: on September 11, 2001, terrorists release VX gas into the New York Subway system.
This one could be quite effective. The Tokyo attacks in 1995 were less than brilliant and still affected over 1000 people (only 13 killed). If al-Qaeda learnt from Aum's mistakes and delivered the VX more effectively they could easily kill as many they did with the planes.
It would be interesting to see how this affected public transport in the aftermath. We had massively increased airport security, it would be hard to implement something like this for trains. This could be a more localised problem though, as the most used subways tend to be in the Eastern US, whereas planes are everywhere.