Appscenter - Allows you to put apps in notification center (for me i put store apps in there to lessen clutter)
SBSettings - Easily the most versatile for customizing your phone. Adds something similar to a notification center that allows easy toggling. Hides icons (like annoying apple stock apps) but doesnt delete them from your phone. Management of processes
Flux, which you can also get for your computer. Dims the screen during certain hours automatically so you don't burn your eyes out checking a drunk text from your mom at 3am .
Also, add this repository: http://hitoriblog.com/apt/ and immediately download FakeClockUp. This lets you set a multiplier to speed up the UI animations by. Basically, it makes navigating your phone so much faster because iOS waits for all these fancy animations to draw out very slowly. It makes it feel like upgrading from a first gen iphone to an iphone 4. (I have an iphone 4, blew my mind). Easily the best app on Cydia.
SBSettings - fast toggling of settings such as Wi-Fi and 3G (free)
WinterBoard - theming engine (free)
DreamBoard - slightly more advanced than WinterBoard (free)
WeeKillBackground Pro - closes background apps quickly (99c)
BiteSMS - adds functionality to the default SMS such as quick reply (free/11.95 no ads)