Your comments

Okay, thanks for the information. That's easy enough to add to my bibtex entries. However, I tried what you suggest and the links to arxiv show up as a picture of a box with a diagonal arrow (same as the plain url field), rather than the 'arXiv' text. Any idea why?
This is excellent, thank you!

I've cleaned up the few instances of commands that don't work, switched the \(...\) back to $...$ (that was just me testing out different things, since $...$ isn't supported by default in MathJax), and now all the titles look great.
I looked into this some more myself, and by including a call to MathJax on my page I am able to get math to display in my title. However, all of the curly brackets are getting stripped out before MathJax has a chance to run, so I'm still left with strange looking titles because something like $^{26}\mathrm{O}$ gets turned into $^26\mathrmO$ which MathJax renders as 26\mathrmO.

Perhaps a simple solution is to allow an option where the curly brackets are not stripped out, for people who want to run MathJax on their pages?