Gaia GPS seems to be the best GPS app I have seen in terms of a good GUI.
Time Calculators are useful when adding up sectors and cross checking entries into various documents.
NAIPS if you need works well.
Aeroweather and iports do similar things (current weather/notams/metars), but Aeroweather has first/last light and iports has some basic runway info which can be useful for prepreplanning.
Worldview app keeps you up to date on webcams if you fly to ports with webcams.
Conversions
World map. Useful for discussions about longhaul flight routes.
Declination - magnetic variation world map.
Save a wunderground safari page as an app icon to go straight to the location group you want
Good Reader - USB upload all your aircraft manuals and Maintenace manuals in PDF to your iphone. Very useful to have to hand.
Notecards - make flashcard question and answers on your aircraft technical specs/limitations or IFR questions etc.
Real Racing full - for overnights.