Auxo
Springtomize 3
iFile
Homescreen Designer
iCleaner Pro
List is great, I personally don't use Homescreen Designer because everything I wanted to change in home screen is possible with Springtomize 3, too.
I would add these Cydia apps/tweaks:
- LockInfo 7 (Enhanced Notification Center and integrated in Lockscreen with a lot of customization options)
- Activator (centralized gesture and function management app, can assign any gesture for any functionality in system)
- CCToggles (enhance and customize the control center, all elements, add apps, actions etc.)