Let's say you have Docbook or DITA content which has embedded MathML equations and you want to properly view the equations in the published WebHelp output.
For my tests I created a new DITA topic starting from our "DITA Composite with MathML" new file template which contains an embedded MathML equation. Then I referenced this topic in a small DITA Map.
The PDF output created using Apache FOP properly displayed the MathML equation so you do not need any customization for it.
As for the HTML output in order to use MathJax I created a file called footer.html with the content:
Then I edited the DITA Map WebHelp transformation scenario and set the parameter args.hdf to point to the footer.html resource.
I transformed to WebHelp and the equation was properly rendered in the browsers I tested with (IE, Chrome and Firefox).