Sunflight. The BEST app for this purpose, hands down.
Let me give a shout out to SUNFLIGHT (NOT to be confused with similarly named SunInFlight) which is written BY a Pilot, FOR Pilots.
Unlike the other APPS mentioned (and I have tried many of them) this APP allows you to input the departure airport, destination, flight times and altitude and VOILA - you get the sunrise, sunset and Prayer times accurate to within a minute or two, and it even shows WHERE the sun will set such that you can set a FIX in the FMC using LAT / Long or it will even display a map of the sunset location on the iPhone for you.
The other apps mentioned all require Lat/Long inputs while SUNFLIGHT already has a worldwide airport database, which makes it great for figuring this out before you fly.
I've been using this APP for 3 years, and been thoroughly impressed with it. The only routes where it ever gets confused is over the pole, but all other trips it's accuracy has been amazing.
itunes dot apple dot com/us/app/sunflight/id447540750?mt=8