Currently, whenever you export to HTML, you have 3 options for processing LaTeX fragments: (1) dvipng, (2) jsmath, (3) or leave it as is.
Is it possible to use an arbitrary program to process LaTeX fragments? What I want to do is use a commandline converter to turn the LaTeX fragments directly into MathML. This way the final HTML document already has the correct MathML without the need to use javascript. (Why? I use princexml to convert that HTML file to a hi-quality PDF. JSmath is no good for that.)