My setup...
Activator: In combination with SpringFlash, I use this tweak to bind the screenshot function to holding the sleep button for a bit, and a double tap of the sleep button to turn on the flash light
Adblock: Pretty self-explanatory
AndroidLock XT: I put it to 0% opacity so nobody even knows that they need to enter an android lock combination to get into my phone.
Auxo: Tweaks the multitasking bar at the bottom to show the last screen you saw in the app, rather than the app's icon. Also adds functionality to the buttons and ipod controls if you swipe to the left
Barrel: Different animations for swiping to different pages at the springboard
biteSMS: A must have. Prime function is quick reply, which allows you to reply and send texts quickly from anywhere. Look it up, it's the perfect replacement for the default SMS app. Also it has some cool themes built right in that make the app look amazing
BlurriedNCBackground: Changes the background of notification center to a transparent, but blurry screen. It's customizable in the settings, but it makes Notification center pretty snazzy looking.
Bolt: Gets rid of the battery icon, I just have a number with a percentage, and a lightning bolt icon. Just cleans things up a bit.
Bulletin: Lets you use notification center at the lockscreen
BytaFont: Apply different fonts that are system-wide (you can see the font change everywhere). I recommend the font Geo Sans Light
clear Lockscreen: Gets rid of the shadow bars and whatnot on the lockscreen
CyDelete: Delete Cydia apps from SpringBoard just like regular apps
f.lux: Adjust the colors of your screen to be warmer; ideally, it'll match indoor lighting and be easier to look at during the nighttime. Customizable.
FakeCarrier: You can make the carrier text in the top right on the status bar into whatever you want.
Five Icon Dock: Pretty straight forward
Five-Column Springboard: Fit more icons.
FolderEnhancer: Have tons more apps inside folders, put folders inside folders, and have multiple pages inside a folder
iFile: Great file manager and viewer
iGotYa: Fantastic security app that can take a picture with the front facing camera when someone tries to guess your password more than 2 times, or if someone tries to turn the phone off while it's locked. It will email you the picture and the location coordinates of the phone. Customizable, and so far very effective.
iMatte v5 Digital Clock Widget: Monitor the time right down to the seconds, plus weather, at your lockscreen. Very sleek, just know that to set the weather to your location, you have to use iFile or SSH to change some data in a file. It'll tell you how to do that.
Lockscreen Clock Hide: Since I have the iMatte clock installed, I don't want the two overlapping. This gets rid of that default clock.
Matte Nano HD: Winterboard theme. Very clean, and it seems to auto trim app icons, so even if they don't have a custom icon for an app, it'll fit right in.
Minimal Slider HD: A more sleek slide to unlock bar.
NCSettings: My preferred alternative to SBSettings. Very sleek, clean look, and customizable. It puts functions like turning WiFi and Data on and off, adjusting brightness/volume, and anything else you could think of in the notification center. Highly recommended.
No Icon Shadows: I don't really need this right now since the Matte Nano theme does this for me, but it cleans up the springboard by getting rid of icon shadows.
NoNewsIsGoodNews: Gets rid of Newsstand, or whatever the hell it's called. It's the annoying one that you can't move but probably never use.
WinterBoard: Apply downloaded themes easily. Comes default with some great features to tweak interface.
That's all for now! Enjoy!