I did made some progress in running Newbler (couple of versions ago) under both Debian and Ubuntu. I needed to fix some of the paths inside launching scripts and GUI was working fine (it's Java based after all and you have it embedded in the package).
However on the long run Debian/Ubuntu might not be the best OS of choice. We had issues with Newbler hanging on Roche's test data (looked like issues with system-specific paralelization, but I might be wrong). If you don't have RedHat, the whole package runs fine under CentOS.
You can also look into SeqAnswers forum what is the current status on Roche's software.
In order to run Newbler's GUI under Debian/Ubuntu, you just have to change the paths for a couple of scripts as described here (http://seqanswers.com/forums/showthread.php?t=1048). I have never had any problem running it under Ubuntu.
The command line, however, works directly out of the box, with no fixes needed.