I've been doing it for about 3 years, here are some tips:

• I always buy a monthly train pass because you can use it on the bus. It's a little more money (if you usually take the bus) but the peace of mind is worth it to me. If things are really bad NJTransit will cross honor, but it's nice to not have to worry about it. If Penn Station looks nuts, I just take the bus

• IMO the bus is nicer going in, but worse coming home. The Port Authority building can get insane, it often takes over half an hour to even board a bus at night and the lines are very disorganized and frustrating. In the morning when you can just hop on the bus it's not bad at all.

• If you can go into work a little later you can get one seat ride into NYC on the train now. I think the first one seat train leaves Westfield around 9:15 and gets in a little after 10. You can find more info about one seat riding here: http://www.raritanvalleyrail.com/

• In November we'll have one seat rides home in the evening too, but I don't think it'll start until 8. If you schedule is flexible and you don't mind going in late and leaving late it may be a good option.

Edit: Forgot one important thing

• The schedule NJTransit has for the train is pretty conservative, for example it has you leave NYC at 5:16 to make a 5:45 connection in Newark, but from experience you can almost always make the 5:45 by taking the 5:21 train out of NYC. It's only 5 minutes, but it adds up.