I may be the odd man out, but especially for the case where I modify a small part of an expression I like MathML because those small parts can be uniquely identified and altered without altering or reformatting the rest of the expression. MathJax supports MathML, so this is possible with MathJax.

For example, the event handler that updates r at the bottom of this page: http://www.vizitsolutions.com/portfolio/gausslaw/ does not know anything about the expression as a whole, it only knows to update elements with a certain class with the new r value.

Of course I will take a look at this and see how it works for my content. It seems though, that this would be a case of interest to Khan Academy as it is comparatively common in instructional material.