Originally, they were to serve as actual transportation on the muck, but it may make more sense to use them primarily as cool sets, at least at first. A network of stops might develop later.
Here's a dump of potential ideas I had, for collective thrashing-out and Function-scrutiny:
With a great screeching of brakes and groaning of metal, a giant snake with blazing red eyes zooms into the station, its jaws agape. As it shudders to a stop, the snake's scales seem visibly faded in places - in fact, where the holocladding has worn off, the gleaming, scuffed metal of the train beneath is visible. Subsequent artists have added their own layers, mostly simple tags and spraybombs. A line of five stony masks, probably scanned self-portraits, stretches down the length of one car. The doors grunt open, squares of sickly fluorescent glow against the scaly, diamond-patterned hide...
Big stretches of abandoned stations and tunnels. Perhaps they connect to the lower level of the Galleria (as they do to the Galleria's non-abandoned RL analogue). Huge tree roots busting through the ceiling. Links to all sorts of other weird tunnels, too.
Further inspiration:
Other ideas? Coalesce has suggested the tunnels hook up with DarkUnder.
Notions: take the idea of a Subway and what it does and take it further. Like a tunnel where you don't enter, but make a faceless copy of yourself and it flies through the tunnel till it reaches some point whereupon it leaves and becomes another you. Or some kind of plexiglass tube where all the passengers are merged together into a great mass. Or this being passes around flyers that, if touched, gradually adds features to the sentient until the sentient is everywhere at once. Then the sentient just has to rip the flyer to get back to 'normal'. Or, and this one I really liked from Edgeworks (an Over the Edge fanzine--I think it's defunct now alas), a Subway where the stations can appear in strange places, like your fridge and under your bed. The best thing, I think, is for you all to just start writing stories about it and see what happens. If I were feeling less lazy -;) I would be writing one now. Zoe