in-app content get backed up to iCloud

I'm about to upgrade my iPhone 4 to iPhone 5 and would like to ensure I take all of my in-app content/information with me. I know that my calendar, contacts and photos on camera roll will be backed up to iCloud and/or my PC but will photos saved in alternative apps be retrievable on a new phone via iTunes/iCloud back up? If not, how do I copy/transfer them to my PC for safe keeping before the upgrade? My main concern is all of the photos saved in folders within my 'Photos + Folder' app (which is brillant for organsing photos!) and my reminders saved in 'Notes' app... Any advice would be appreciated. Cheers.