I have NCE at home. We run Digitrax at out club. I like NCE better because it is more intuitive to use, the buttons on the throttles are larger, and the instructions are better. Both systems have a good upgrade path. If you are going to have a medium to large model railroad and you are thinking about operations with friends, the NCE 5 amp Power Pro system will be easier to set up than starting with a smaller system and then adding components to it to make it a larger system.
For a little extra money, you can use the Digitrax signal system with your NCE system, if you get that far. Here is a link for that if you are curious:
http://www.waynes-trains.com/site/Signals/GettingStarted/SignalsGettingStarted1.html
The link at the very bottom of the page is what you are looking for.
You also need to read this thread: http://cs.trains.com/mrr/f/744/t/216089.aspx