[G3 General] if4ct0r:
Here is my setup at the moment:

Google Now Launcher + Xposed GEL Settings module - I've grown to love the Google Now Launcher with the Google Now integration so much that I'm just not happy with any other launcher. This Xposed module is a must have for those who wish to have most of the customizability of other launchers while using this launcher.

Greenify + Greeniy Xposed module enabled - Needless to say, possibly the best auto-hibernate-app utility out there. Helps with battery performance a lot.

SDMaid Pro (ROOT app) - Has a bunch of really useful utilities for cleaning duplicate files and maintaining the SD card in a clean state.

ROM Toolbox Pro - Used to be really useful in my old days of HTC Desire HD, customization features work well with CM ROMs. For now I use it occasionally for the many built-in apps including a terminal emulator, root browser, startup manager, build.prop editor among some others. Useful apps to have in one place.

Tasker - Needs no description. The most powerful automation tool ever! I use it to automatically change my wifi, data, sound & brightness settings based on whether I'm at work, home, sleeping or reading something on my phone.

G3 Tweaksbox - Thank god for Tweaksbox & root. With the unlocked bootloader I would've grown pretty frustrated if not for this. Currently using the Tweaksbox for UI Themes, Nav Bar color, Bigger caller picture, battery notification tweaks (especially that annoying wireless charging notification), etc. One of the most useful features I find is the Misc. Tweaks > "Enable Knock Off on Nav Bar" - This allows to knock off the phone by just tapping on the nav bar instead of all the way up at the status bar when using a non-stock launcher like I do. Also helpful is the feature to change the default messaging app color(hate the yellow!) found under "Message Tweaks > Theme color".

Network Speed Indicator (Xposed Module) - I like to monitor the network speeds when using the phone and for the time being when there is no support for this feature in Tweaksbox, this little Xposed module comes handy. Offers some customization as well!

Unicon (App/Xposed Mopdule) - Another must-have on any rooted phone that I have. Allows the use of icon packs on any launcher including the Google Now Launcher that I use. Changes the icon system wide. Great app!

You-tube AdAway (Xposed Module) - Gets rid of the annoying ads that popup now and again while playing vids on YouTube.

AppSettings (Xposed Module) - Allows changing per-app DPI for when you change you phone DPI and some apps get messed up.

I guess the above classify as tweaks, but while we're here, here are some apps that make my life a bit easier:

Talon for Twitter - UI customization, In-app browser + video. Used to use Falcon Pro but this one is equally good if not better with multitude of theme options

Unclouded - Keep tabs on your cloud storage accounts in one place. Useful.

Zooper Widget - Must have for theme & UI customization fanatics.

Sidebar / Switchr - Both from the same dev, both offer options to switch between apps from any screen. I used Sidebar before, Switchr offers much more now. Both are worth a try.

LinkBubble - Really really useful for surfing various links from say, your twitter feed. Loads links is a small bubble while you continue to do whatever you're doing. It's one of those you-don't-know-what-you're-missing-till-you've used-it features.

VSCO Cam - Really great alternative to the stock camera app. Offers much more editing features.

HeadsUp - If you've been missing heads-up notifications from CM/PA ROMs(like me) this is a nifty little app that brings over the functionality.

There. Most of them are probably well-known & that was a long post, but I hope it helps someone to find something new and/or useful :)