I've used both and I greatly prefer python+scipy+matplotlib. Because it's a real programming language, unlike Matlab's clunky Basic-like thing. So if matplotlib

I've used both and I greatly prefer python+scipy+matplotlib. Because it's a real programming language, unlike Matlab's clunky Basic-like thing. So if matplotlib doesn't do what you need, you can extend it or just write something custom in GTK+Cairo. The depth and stability of scipy & matplotlib is very impressive.