I'm quite a fan of subway photography and have a set of subway photos on Flickr, as well as a public group I founded, which now has 45 members and some great photos.
I just happened across this set by mcbnyc, who takes a photo of every subway train he rides as it arrives. Looks like he often rides the same line I do.
I stumbled across mcbnyc's efforts reading this thread about the legality of taking photos on the subway. It is legal, but apparently MTA employees regularly harass people taking photos, threatening to fine them or have the arrested. Earlier this year, photographers met in Brooklyn to protest MTA harassment.
The MTA's Web site actually explicitly allows photography, though if forbids tripods, unless you're a member of the press with identification.