I (second) vote for R. I have no idea about any graphical interfaces to it, but having used it command line wise (which is, I assume, how one is supposed to use it?) I can recommend it. Well of course you'll have to know what you're doing, but that's something you have to know anyway, right?
Plus, the way R works, it's easy to write scripts/programs for/with it, even if it was just one piece of the puzzle.