It'd be advantageous to list our favorite root apps so new people (to rooting) know what they can do. Some apps have free or paid versions. Sometimes paid versions are just for donations, sometimes you get more features for 'donating'.
SuperUser Elite:
SuperSU:
SuperSU Pro:
BusyBox:
Adfree:
MyBackup Root:
Titanium Backup:
ES File Explorer:
Root Explorer:
Autostarts:
LBE Privacy Guard:
DroidWall:
Permissions Denied:
MSL Reader:
Webkey:
Boot Manager / Boot Manager Lite:
CacheMate:
Chainfire 3D:
closeFeint:
Quick Boot:
Roam Control:
Lite Flow Lite:
SetCPU:
SuperUser Elite:
This is a more advanced version of SuperUser that gives advanced logging and pin protection. Good for us paranoid types.
This new version of SuperUser, from Chainfire, gives more options than SuperUser. It has interesting features, like unroot and can even temporarily unroot, and some security upgrades.
Gives more advanced options than normal SuperSU. Including an OTA survival option.
Many root apps need the tools contained in BusyBox. A good thing to install right off the bat.
God, I've missed this. This installs a hosts file into your Android system that prevents the phone from loading ads.
A backup program for your apps, data, contacts, etc. Simple to use, but not as feature laden as Titanium Backup.
The infamous Titanium Backup makes backups of your apps and the data contained within them. This means you can back up your Angry Birds progress, high scores, among other things, like settings. Also allows you to freeze apps (with purchased version). Freezing is like putting apps on pause. Useful for bloatware you may want to use in the future. Highly recommend getting paid version.
An all in one file explorer, including a root explorer. Completely free.
You're going to want this, eventually, if you plan on making any changes to the directories. Like boot animations and other mods. This is a pay-only app.
Prevents apps from auto loading when certain conditions are met. The primary one being when the device boots. But there are more conditions than that. Definitely worth a buck if you want to stop apps from auto loading.
An advanced privacy program that can block internet requests, contact request, locations, etc from apps that you don't want to have them. Easy to use
A firewall for Android. Prevents certain apps from using the network without turning the network off.
Deny permissions to selected apps (user installed ones only, not system apps). Be careful, though: Restricting permissions may cause the app to behave oddly or force close.
Get your MSL code so you can change phone settings in ##DATA# and other places.
This app allows you to control your phone through a browser. I've never used it, and personally wouldn't trust access to my phone to a website, but the option is available if you want it.
Allows your device to have multiple ROMs installed on your SD card so that you can try new ROMs or have a multi boot like configuration for your phone. Your phone must be S-OFF for this to work properly. Will not work with HBOOT 1.5.
Allows you to quickly clear out the system caches. Use this if you think your phone is responding sluggishly.
Hate how nVidia chips (the Tegra 2, specifically) get game exclusives? Chainfire seeks to rectify that. Unknown if it actually works for the 3vo so far. Don't let the 3D in the name fool you, this does not use the parallax barrier to make games utilize our glasses-free 3D effect. It just makes Tegra2 games compatible with our devices (if it works for 3vo).
If you're like me and hate openFeint with a passion, this app is for you. Disables openFeint from slowing down your games. Deal breaker: Is not compatible with Adfree.
Enables you to reboot your phone quickly, including into recovery.
While technically you didn't have to have root to be able to use this app for HTC devices, some may not be aware of it. Allows you to switch over to the VZW network.
Allows you to manually set the behavior of your LEDs.
The seemingly most preferred CPU manager app out there. Used for overclocking/underclocking and governor modifications.