Sixaxis Controller is an amazing app for any gamer. It allows you to sync a Sixaxis controller (PS3 Dual Shock 3) via bluetooth rather than having to connect it directly into your device with an OTG cable.
This is awesome because you can use the controller wirelessly and use an MHL 2.0 adapter to play on the bigscreen. Sixaxis Controller also allows you to emulate touch and create your own profiles for each individual controller button. Making games that aren't compatible with controller's work. (Modern Combat 4, Order & Chaos, Ravensword, etc.) You can find game mapping here on XDA for the app.
Greenify is great for saving battery life and keeping your phone nice and speedy. It disallows apps you choose to run in the background uncontrolled; definitely an app for any rooted user!
If you flashed your kernel as well I'd recommend Trickster Mod, It's a pretty generic tweaker. The built in profiles can help tremendously in saving battery life, and game performance for helping with frame rate issues (though the S4 shouldn't have any). Depending on your kernel you can also use the tool to OC (Overclock) your CPU, GPU, and voltages. But be very careful if you decide to do any OC'ing, as it could brick your device.
Titanium Backup is great for uninstalling any bloatware you may have on your OS (if you're using stock TW that's rooted). You can also make backups of your system for recoveries. The pro version offers a lot more good features, if you want to pay for it.
Root Browser is a nice neat file manager for rooted users. It has built is ROM features as well as being able to deal with opening and zipping .jar, .zip, .apk, etc. It's really nifty.