Since this month our application note is published online (http://dx.doi.org/10.1007/s13127-011-0056-0). Please cite it, when you use raxmlGUI.
Silvestro, D. and Michalak, I. (2011) raxmlGUI: a graphical front-end for RAxML. Organisms Diversity & Evolution. DOI: 10.1007/s13127-011-0056-0
Thanks for your support!
We plan to upload a new version early next week with some new options and one major gimmick: you will be able to construct a concatenated data set from within raxmlGUI by adding alignments one by one.