I have found a very nice Open Source software (with GUI) that is available for Linux too. It's called Free Audio Converter or fre:ac (former BonkEnc) and it is able to use external encoders, thus it can also use Nero's CLI (NeroAacEnc):
To have Nero encoder available as CLI in terminal, you have to put it in usr/bin and make it executable:
additionally you should also copy Nero's AAC tag tool there:
sudo cp neroAacEnc /usr/bin
sudo chmod +x neroAacEnc
Then open terminal to test if Nero encoder is there and see all available options for usage:
sudo cp neroAacTag /usr/bin
sudo chmod +x neroAacTag
In case it says it can't find the file, then you're obviously running a 64-bit system. But the Nero encoder is 32-bit. To fix it, install:
In many cases this is not needed, as other software might have installed this dependency already. But on a fresh install of 64-bit Ubuntu, Nero will not work unless you install this dependency.
sudo apt-get install lib32stdc++6
If you have neroAacEnc already in your usr/bin directory, fre:ac will automatically find it and provide it as an encoder option.
Alternatively, you can also put the neroAacEnc in fre:ac's directory under codecs > cmdline (and you have to make it executable of course; just right-click the file, choose properties and under 'Permissions' check 'Allow executing file as program'):
Project's official homepage:
Linux snapshots vailable here, for both 32-bit and 64-bit:
The binaries work out of the box in Ubuntu 12.04.