Cross-Train is all about getting you around the subway and railroad as quickly as possible. It finds you the fastest trip, taking into account any express trains and transfers that may save you time. It does all the processing in the app itself, so you don't need a data connection.
Did you know, if you miss the 5:23 PM Penn Station to Ronkonkoma train, you can take the 5:24 Babylon train and catch up with it at Jamaica? Or if you miss the 5:59 PM Penn Station to Copiague train, you can take the 6:05 Wantagh train and transfer (to the train that left at 5:55 PM, actually), getting you home 15 minutes earlier.
There are apps that already tackle schedules for the LIRR and Metro-North. Cross-Train finds you shortcuts, and takes on the subway too, and connects it to both. You're in the subway. Is it quicker to take the next train, or wait for an express? You're downtown, and want to get back to Long Island: is it quicker to take the subway up to Penn, or over to Atlantic Terminal? Is there another way you didn't even think of (Forest Hills, Woodside)?
Cross-Train gives you the fastest way around the subway, LIRR, and Metro-North. Windows version available now; Windows Phone version is pending app store approval: check the website for the latest info.