Waves
Boot Logo
Ace El Cap theme
Lockscreen
LockHTML4
Custom Notification Start: 255
Lock + for LockHTML
Coordinates: X: 0 Y: 75
HideMeX (To Hide Elements)
Xen (http://repo.incendo.ws) (Install BetaVendor from said repo to install)
Kecil Passcode theme (http://colbyroark.yourepo.com)
SleekCode (Remove borders around numbers, remove letters)
HideMeX (https://repo.cpdigitaldarkroom.com) (Remove Emergency and delete buttons, remove passcode text)
CustomCover
Veexillum 2 theme
EW2.MusicControls (http://evelyn-ynam.yourepo.com/) (Media controls)
Acapella II (Hide some music control stuff)
Springboard / Homescreen
Licek Theme: http://colbyroark.yourepo.com (I edited some unthemed icons myself)
Boxy 2 (Icon layout)
ColorBadges [White badges (they change badge color based on app icon, but I have uniform app colors)]
Springtomize 3 (Hiding stuff)
HideMeX (Hiding stuff)
Cylinder (Changes animation of icons when swiping through springboard pages)
Upscale (http://repo.bd452.com)
CustomFolderIcons (To edit folder icon at the bottom)
ClassicFolders ("App Launcher" layout)
Wink (to hide the statusbar)
Control Center
Veexillum theme
Acapella II (Gesture based music controls)
SimpleCenters (Clean up CC elements, such as dividers and toggle backgrounds)
Uniformity 2 (http://repo.pnre.co) (Change app toggle colors)
DarkCC (http://leftyfl1p.github.io)
Notification Center
SimpleCenters (Clean up NC elements)
Carrot Weather Widget: Link to App Store
Fantastical 2 Calendar Widget: Link to App Store
ColorBanners (Not shown here, but colors the headers of notifications)
HideMeX (Hiding Stuff)
Springtomize 3 (Editing stuff)
Notifications
WatchNotifications (Notification style on LockScreen)
ColorBanners (Colors notifications; I set it to one color for all apps, but colors notifications based on app icon by default)
Couria (iOS 8 & 9) (iOS 10-esque quick reply menu for Messages App)
Roundification (http://zachatrocity.com/repo/) (Rounds notification banners on springboard) (Get it from the beta repo to fix UITextField bug)
Xen (http://repo.incendo.ws) (Install BetaVendor tweak to get Xen) (Better Priority Hub, along with other really cool features. Check it out)
Messages App
Messages Customizer Pro (Changes background, dark theme, etc)
Saber (Actually Lancer, but it's included) theme (repo.tsunderedev.moe) (Line theme for messages)
Cydia App
TranslucentCydia (Blurry background)
Codling (Blurred Loading)
DismissProgress (Exit Cydia installing view)