I'll look into it! I'm planning to get on at least every one of the colored subways once. Also gonna get a MetroCard - I can use it to get on the train from Jamaica to Penn too, right? Getting to Berlin is gonna be sweet too, since most of the trip is in a nice ICE train. Hotel is right on top of a U6 station. Don't have too much free time though, there's a reason I gotta be there.
You can use your Metrocard on the SkyTrain (from JFK to either Jamaica's megastation or to Howard Beach on the A train) and on buses and subways, but not on the LIRR (commuter train). The easiest thing to do is buy a Metrocard when you get to the SkyTrain station at your terminal. Put both a week's pass and $10 on it. The first $5 will be taken when you exit the SkyTrain turnstiles at Jamaica (it's free when you're going from terminal to terminal, but they charge you at the non-terminal stops). The weekly pass will kick in when you first ride a bus or subway. While you're exiting Jamaica's SkyTrain station, grab as many maps as you can. The subway map is obvious. However the borough bus maps are also really good walking maps. Get two Manhattan bus maps -- one to mark up and another for your wall.