Sounds like the Yamanote. You're lucky you got off at Shinjuku. The segment of the Yamanote between Shinjuku and Shibuya is said to be one of the most crowded in all of Japan.

That's another good reason to live outside the loop. You can usually avoid the Yamanote altogether. Some of the lines radiating out from Tokyo are just as bad. But many are not. It might behoove one to ask come colleagues (or experienced train riders on this list) about certain segments once you know where your office is and have a potential apartment picked out. I always said I was going to try a test-run at rush hour before relocating but never had the time or inclination to follow through on my threat.

I guess the point is that you don't have to be shoved into the train by the "white-glove army" if you plan ahead when picking a place to live and avoid the segments that everyone in the city uses (like Shinjuku-to-Shibuya or Shinjuky-to-Ikebukuro... or any part of the Ginza-sen ). It also helps if you're in a position to be able to skew your work schedule a bit one way or the other to avoid the heavy times (which seem to be different on different lines).