Not sure if I did something wrong, but here's what happened for me:
1. Unlocked boot loader using adb and fastboot oem unlock command, went fine
2. Downloaded Superboot
3. Ran install-superboot-windows.bat
-- Phone rebooted (Google lock screen was only up for maybe a second, seems weird since everyone else had to wait minutes...)
4. Checked to ensure SU was installed and root was given.
5. Installed some root apps (TI backup, RootExplorer, etc...) All work fine, messed around with TI backup and RootExplorer a bit
-- Noticed every time I reboot I get a screen that says "Upgrading Android" Hmm...
6. Installed the OTA update 4.0.2
-- Some apps no longer have root access? Can no longer update SuperUser (fails at "Gaining root access") or run TI Backup (no root access), but RootExplorer still runs fine and SAYS it's been given root permissions... I also no longer get the "Upgrading Android" screen.
Not sure if I should try again, because I really didn't like that "Upgrading Android" screen on every boot...
This is all with the VZW Galaxy Nexus, by the way.
Can anyone confirm if I do the update 4.0.2 that im getting on my device now (after i unlocked bootloader and rooted) If I will loose root and bootloader unlock???
Personally I rooted post-OTA, but I'm guessing if you OTA after root then you will have to re-root. At least it's been this way with every other Android phone I've had.