Beyond the normal gross stuff that happens underground, I have three particularly memorable incidents that have occurred on the subways over the years.
1. Several years ago, at Penn Station, this weird drifter was standing near the turnstiles muttering incoherently. I went through the turnstile, and looked back. He made eye contact with me, said "I'll burn you. I got flame," and held a lighter towards me at arm's length.
2. Looking down at the track of the E train, these two rats were chasing each other. Suddenly, they met in a warm embrace and started humping away atop the rail just seconds before the train blew into the station.
3. This past Tuesday, I was walking from the LIRR to the 1/9 train uptown. (It has actually been renamed the 1 train, because they realized that the 9 train took an identical route.) There's this one area near the stairs that smells like, well, an abbatoir. Every day. It just reeks. It's this closed room next to the elevator.
On Tuesday, the floor in the passageway was wet. There was almost an inch of water on it, and two workers had those big scrubber machines trying to move the water towards a drain. The room itself had sprung a big, garbagey leak. Water was squirting out from between every tile on the bottom 12" or so of the wall.
If anyone out there is actually reading this, and is from New York, I have a challenge. In the comments, tell me about your worst mass transit experience.