In light of the recent incident on the D train, in which a man was stabbed and fellow straphangers were locked in a car with the murderer, this Slate article on the history of subway studies is worth a read.
Subway cars have been used for psychology experiments for decades, and the context for many in the 1970s was the Queens murder of Kitty Genovese, "whose cries for help were purportedly ignored by her neighbors... [her] story became the ur-narrative of uncaring urban pathology. The subway offered a perfect testing ground for the emerging subfield of bystander studies." One study found that the more bystanders present, the more likely it was that someone would help.
On a more normal, drama-free commute, crowding levels have been linked to higher stress levels. And your oblivious physical contact might mean something too! One study says that "elbow manipulation becomes one way of expressing sentiment concerning the person sitting next to you," as does hand position on the poles. As far as eye contact goes, "commuters were more gaze-shy in the city," than in the suburbs. Studies found this isn't because we're rude, but because we have too much to take in and process — or as they put it: "interpersonal overload leads to social withdrawal." Sure... that, or iPhones.