+1 for getting Root Explorer. It is an amazing root file manager that has so many features.
If you havent bought Titanium Backup yet check out the app "AppExtractor". It allows you to Resotore Apps/Data (System/User), SMS/MMS, Contacts, Wifi Settings, Bluetooth Settings, and Bookmarks from your nandroid backup. With the paid version you can Freeze/Unfreeze system apps, Extract a single .apk, and fix permissions. Ive been using this app for awhile now and am very happy with it.
Another nice app to have if you use franco's kernels is his updater app. It checks for updates to his kernels and downloads them. You can have it auto flash the kernel or it will download the kernel as a flashable zip. It has all the features of other overclocking apps such as max/min settings, govenor selection, and voltage control built in so you wont have to use another app to change these settings. There are also other settings like color control where you can change the RGB settings for your screen.
CPU Spy will allow you to see how long your phone has spent at each of the clock settings. It is useful to see if your phone has been entering deep sleep or not.
Boot Manager is fun. It took me awhile to finally get it working correctly, but with the number of different rom choices for the gnex it is great to have. It allows you to install different roms onto your sdcard and boot into them with the press of a button while maintaining your main phone rom. I was hesitant about paying for this app, but am happy with my decision after using it for awhile.
These are just a few apps that I have been using for awhile and use more frequently than others.