The LIRR does very well considering that they are at capacity on a large majority of their system (or at least the parts of the system that are the most important) Not to mention that their busiest station and primary western terminal is run by the almighty National Passenger Railroad Corporation (Amtrak) of which the LIRR is subject to the whims and desires of.
Furthermore the timed transfers at Jamaica are great. Can you think of any other railroad that operates three terminals and orchestrates the schedules to line up in such an awesome way?
The LIRR has begun to excel in communicating information to passengers. All stations now have the AVPS system (destination screens, automatic and manual announcements, the works) and they have improved their e-mail and social networking systems.
Metro-North is another quality railroad. They do seem to have their act together when it comes to operations. They've been expanding service off-peak and on weekends, adjusting service patters and trains to fit the needs of their passengers, and not to mention that Grand Central beats out Penn Station in terms of niceness in just about every category,
NJT, let's just say I don't hold this system in such a high regard as the others. They do run the NEC (and probably most of the Newark Division for that matter) pretty well. They have good service patterns, decent peak express service, and the like. The off-peak service leaves a lot to be desired. Crowded trains that are either too infrequent or spaced too close together to do Amy good.
Now the Hoboken Division, that leaves a lot to be desired. Yea, it moves a lot of people, but there are defiantly ways to make it better. Some of the stations are way to close together (the 14 stations in the Oranges and the 108 in Montclair...) so that makes speeds inbetween them abysmal.
Furthermore, NJT's fare system is all confusing. With the two divisions having different fare structures, different ticket prices for the same distances traveled, change in terminal fees, how havinng a SEC ticket costs more than a NWK/HOB ticket even though you're going to the same place, hold-down fares with Metro-North, how weekly rail tickets are only good for one bus zone even though they're valid on the HBLR which requires a bus pass valid for two bus zones, how peak fares apply only on certain lines to or form certain stations in certain states, and more. Someone needs to do an 'ol "Ctrl+A, Backspace" on their tariff policy and start over.
SEPTA has often been nicknamed INEPTA, enough said.
I haven't ridden too many other systems enough to offer valid opinions on them, other than my brief encounter with the MBTA subway system, where I had to wait 15 minutes for a lady to get out of the bathroom to give me a CharlieCard and then when I went to go put $6 on it, put in a $20, the machine gave me $5 back (subtraction's too difficult for it, I guess). If that's indicative of how their commuter railroad works, it makes me wonder how Bosteners stay sane.