Favorite root apps and ROMs for Android?
ES File Explore or Root Explorer - both are file managers that with root access allow you to easily navigate around. Root Explorer is better for opening APK, ZIP files and the like while ES is a little easier on the eyes.
Apex Launcher or Nova Launcher - both are equally good and incredibly robust in options for a launcher. Very much what Launcher Pro was before the development stopped on it. It's a matter of preference of which is better.
EXT4 Touch Recovery or CWM Touch Recovery - if they're available for your phone they're worth it. I thought I'd hate touch recovery options but it's much easier than dealing with vol up/down and the power button when navigating.
No Frills CPU Controller - dead simple app for controlling your processor with a new kernel.
I don't run a lot of root specific apps beyond the above mentioned anymore as not a ton of them are needed like they used to be. Also a large share are for very specific things that just don't interest me.
While I don't have a Galaxy Nexus I have heard some positive things about Gummy ROMS. I have used MIUI on my own phone and MIUI is also an incredibly smooth ROM. The launcher is very much an iOS feel where there is no app drawer and all apps get sorted how you want. There are are ton of custom themes and lock screens which make great if you're into that but be warned they're mostly ports so some lack translations.
I forget if it's in AOKP or Nova launcher but one of them allows you to modify the soft key nav at the bottom of the Nexus to any shortcuts you want, even a 5 row launcher.
Also, you can customize the UI in ways you can't with the stock OS. Most people probably don't care, but it's been useful for me to be able to tweak the notification drawer or add a dedicated search button to the navigation bar.
- OTA RootKeeper: https://play.google.com/store/apps/details?id=org.... [This was especially nice to have when the Android 4.0.4 update came down the pipe last night; allowed me to one-click restore my root access.]
- Titanium Backup: https://play.google.com/store/apps/details?id=com....
- Hosts Editor Pro: https://play.google.com/store/apps/details?id=com.... [Installed this to make local mobile web development a lot easier, but having access to your hosts file is always nice.]