Hurricane Irene raised the level a lot of rivers and streams in the area, flooding areas like Conshohocken. It also caused Assunpink Creek, which is right next to the tracks at Trenton Transit Center, to flood the tracks almost to platform level.
Unfortunately, SEPTA never moved its Push-Pull train, which is usually parked at the station during the weekends, as well as at least 4 Silverliner IV trains when the creek flooded well over its flood stage.
The Times of Trenton grabbed this picture of the trains still parked in the water:
NJ.com has more pictures of the flooded station: http://www.nj.com/mercer/index.ssf/2011/08/trenton_transit_center_floods.html. To this day, train service has not returned to Trenton, although NJT is running between New York and New Brunswick and the Trenton Line is running to Levittown Station from Philadelphia.