Installer - Installer is a package manager build specifically for iOS. Older versions of Installer are Open Source
Cydia - An alternative app store for jailbroken devices.
iNoJB - iNoJB, formerly iNoCydia, is an amazing Cydia alternative requiring no jailbreak!
Zestia - Zestia is a mobile app designed to assist you in organizing your hectic schedule, social life, and professional persona.
Hydia - Hydia is a non-jailbroken version of cydia wich allows you to customize your device in many ways.
BuildStore - Safe and trustworthy alternative app store for iOS