If you would like to flash your phone with either stock or custom ROM you should have these apps keep inside your external SD-Card or setting. This is what I did....
1. Calendar and Contacts saved to Google. Go to GMail
2. SMS saved to Google using SMS Backup+
3. Backup your current apps using File Expert (including System Apps)
4. Save your document/note using EverNote
5. Auto upload photo while charging + WiFi using Google+
-Keep files to ROOT + BusyBox + Safe Kernel + CWM in the external SD-Card
-Copy your related data folder into external SD-Card such as iQuran folder (too big to re-download)
-With this you will have no problem to Format your Internal Storage and the main thing is you need to have EXTERNAL SD-CARD and the best at least same size as your internal.
-Simpler way is using Titanium Backup.
-I'm not using Titanum Backup because I would like to have clean/new app installation
-Titanium Backup sometimes generate issue to your new installed ROM
-You need to login and configure your apps again (If apps did not have backup and restore setting option). Most of the time I need to restore email setting (2 email server only)
-Most of the apps nowadays have the setting save in the cloud such as FlipBoard, EverNote, Dolphin Browser, etc..