Working Tweaks I have so far on my 6S+. Will update as I add more.
Fascy (faster Safari scrolling)
Barrel (add various animation effects to the icons)
HideMeX (IOS9) (hide unwanted apps, doc background, change carrier name and change slider name, Hide labels, plus many more)
SwipeSelection Pro (swipe directly on the keyboard in order to move the cursor to edit text)
iCleaner Pro 7.5.0 (clean cache and preference files)
iFile (file manager)
ColorBadges (changes badge color to the app color)
No Yahoo! & TWC (removes Yahoo and TWC name in NC, Stocks & Weather)
Minimal Hosts Blocker (a minimal adblocker for IOS) The developer ReddistDream is fantastic!
SaveGram (enables you to save Instagram photos)
Spin (music player-spinning album art and controls on lock screen)
ColorFlow 2 (IOS 8.4+) (modifies the music app, lockscreen, and Spotify app to match album art)
No iAds (blocks iAds)
http://iostonykraft.github.io/
Shortcuts (Uses Force touch menus to add more options in icons such as Settings, Cydia, Weather, Spotify and more)
http://repo.cpdigitaldarkroom.com
YouTube++ (makes YouTube easier to use, allows ad blocking and video downloads)
http://beta.unlimapps.com
PandoraPro (Unlimited Skips, No Ads, No skip delay, higher bit rate, high quality cellular, no jailbreak detection, pandora one splash screen)
http://iostonykraft.github.io/
Anemone (theme manager)
Icon Renamer (rename Icons, i leave the labels blank to un-name icons on my home screen icons to match no labels on my dock)
Slide2Kill9 (slide switcher to kill all open apps at once. Can use 3D Touch to close apps on 6S's)
TWBEnhancer9 (most wanted features for Tweetbot4)
Avier for IOS9 (theme)
ADBlocker 2 (AdBlocker for Safari and other apps)
Cou (shows decline and answer buttons on the lock screen for incoming calls)
Weatherboard 2 (Animated weather on home and lock screen)