http://www.mh-aerotools.de/airfoils/index.htm is a great resource. It has quite a few programs for model aircraft design. Noteably, JavaFoil a 2D airfoil analysis tool, JavaProp, and Java Pipe. There are also many other programs available on Dr. Hepperle's website. You just have to look around a bit. A one i find handy often is the aerodynamic center calculator.
And for the more advanced and adventurous out there, AVL is a great 3 dimensional aerodynamic analysis tool. Google it. You'll find it.