It's not really an app, but CyanogenMod is one of the most popular tools in a rooter's toolbox. CyanogenMod actually replaces the firmware, or ROM, in your phone's flash memory, providing a new foundation that strips away bloatware (those aggravating, preinstalled apps that you never use and can't remove) and adds all sorts of new functions. In a word, it's a stripped OS with some of the most desirable apps built in.
CyanogenMod offers up a sleek graphical interface that's highly customizable; you can choose from numerous interface themes that give your phone a splashy look. It lets you play back FLAC (Free Lossless Audio Codec) music, which audiophiles prefer to lower-quality MP3 files.
With CyanogenMod, you'll have integrated options for overclocking your CPU, which basically means you can squeeze faster performance out of your device. In addition, it offers built-in, incognito Web browsing, gesture-based screen locking and a graphic sound equalizer.
In short, CyanogenMod provides a solid framework for any rooted Android phone. Then you can add and mix different combinations of apps as you see fit.