This is a list of my current tweaks (Descriptions for those looking for a quick reference) with a couple of shout outs to a couple of other things. Please do your research before using any apps to avoid any mess ups.
Action Menu > Quick input shortcuts when typing.
Activator > Shortcut genius (On screen swipes, buttons, all customizable to your liking.
AndroidLock XT > Android style lock code
Animate / AnimateAll > Animated boot logos
Appcent > Percentage progress of app downloads
Appinfo > Displays information on almost anything installed on your phone.
Apple Ad ringtones > ringtones used on Apple commercials
Auxo > Re-imagined multitasking substitute
Barrel > Different effects while switching app pages
Bars > An improved signal strength meter
Bitesms > Turns Imessages into what it should be (Currently using Biteliquid theme)
BlurriedNCbackground > Blurried effect on your notificationcenter / Change color.
Browser changer > Changes your default browser.
Bytafont > Gives you a one stop shop for all your different fonts.
CameraTweak > Adds a bunch of amazing tweaks to your stock camera app.
Color Keyboard > Allows theming of keyboard.
Dater > Adds date and info to pictures taken for future reference.
Dismissmykeyboard > Allows for ipad like dismissal of keyboard.
Double At > Double tap @ to quickly inset email address
EmojiPro > Adds more than 300 emoji icons to use with your texts.
f.lux > warms colors at night so its easier on the eyes.
Fastlock > shortcuts on the lockscreen
Flagpaint > Paints banners based on the icon color
FolderEnhancer > improves and extends folders
Forecast > Forecast replaces the standard lockscreen clock
Fullforce for phone > forces apps to show in full screen (Usefull for iphone 5 users)
iAP Cracker > Free inapp purchases (Useful for games that require actual purchases for stuff)
iBlacklist > firewall for phone calls and messages.
iCleaner > Iphone cleaning and tweaking app.
Iconclasm > Customizable icon layout
iFile > File manager for apple
iProtect > password protect any app
MultiIconMover > Quickly move multiple icons at once.
NCRam for notificationcenter > Quick view of your ram
Nowlistening > Show playing song in notification center with activator.
NowNow > replaces SIRI with Google search
PasswordPilot > Auto inserts your app store password when downloading apps.
Speed intensifier > Speed up your animation transitions
Springtomize 2 > Loaded with springboard tweaks that are very useful
Statustab > allows you to preview your notification bar when in full screen
Swipeselection > Allows you to move your curser when typing by swiping across the keyboard.
Torch > Adds a quick button on your lockscreen to toggle flashlight
TypeStatus > Imessage typing indicator to let you know someone is writing back to you even if you are not in the imessage app.
Wifi booster > Network lists shows all wifi access points.
Winterboard > What allows theming of your springboard.
Zephyr > Swipe multitasking and gestures.
Zeppelin > replaces carrier text with custom icons.
Batterydoctor pro > Cool battery stats app with amazing notification center toggles. (Don't think it actually improves battery life).
%hook's law > Increases reaction speeds (Be very careful messing with the settings, note down defaults)
3G unrestrictor 5 > Allows me to use facetime and other wifi only functions on 3G.
Current favorite springboard themes: Ayecon, Jaku, MiOS.
Current favorite keyboard theme: Phatbook Air CK HD
Favorite case: Incipio Dualpro shine (These people make the best apple cases by far).
Notable mention apps: Appgratis (One free paid app a day), Appsfire (Another application reference app ), Camera+ (Amazing camera substitute), Vlingo (Useful for when driving. Kind of like SIRI.)
Favorite games: Jetpack joyride, Plants vs Zombies, and Subway surfers.
Hope this helped those jumping onto Iphone recently.