In 2005's Batman Begins, Thomas Wayne and a young Bruce go for a ride on Gotham's new train system to Wayne Tower. As Thomas notes, he designed Wayne Tower to be the central hub for Gotham, so all of the train, water, and power lines run through it. This becomes important in the climax, because if a microwave emitter on one of the trains makes its way to Wayne Tower, Gotham's water system will be destroyed.
The New 52's Batman #2 (October 2011) notes that Union Station, aka the central hub for Gotham rail lines, lies beneath Wayne Tower. No word on utilities.
As noted in the article I've previously linked to about Gotham's architecture, this tower first appeared in Anton Furst's concept sketches for Batman (1989), which makes it one of the few canon immigrants to survive the New 52.