From JSXGraph Wiki

Below are the default values for many parameters of a JSXGraph construction. These values have to be overwritten before the initialization of the JSXGraph board via

JXG.Options.text.fontSize = 14;
JXG.Options.text.useASCIIMathML = true;

or more compact

JXG.Options = JXG.merge(JXG.Options, {
    showNavigation: false,
    point: {
        face: 'x'

If you have some more options you want to use for more than just one construction you can save them in an extra .js file and include them right after loading JSXGraph.

The complete list of default can be seen in the latest version of Options.js which available at [1].